Considering that you have less than eight days of deployment time, i doubt they will ever be far enough from the mothership for it to matter.  Maybe use two 25% size launchers and add magazine instead?

On somewhat related note, i would also cut out the engineering spaces out of the 250t one and tried to fit something more usefull. 

Yes. Something that's also driving me nuts is the engine. 2 engines, 2.0 power, 30000l fuel is good for 8000km/s and slightly longer range, on the same size.

So, I took Father Tim's advice... well, a little bit. I still wanted a "true" multi-role fighter, so I retained a 500-Ton version of the Javelin-Class and simply called it the Javelin II. They are different enough from the rest of my entourage [I'm developing an entire fleet at once, may post it here, might now, so take these with a pinch of salt or two... or three.] that they don't need to be of a lower tech to justify their existence. I intend to first develop several 40,000 RP-Cost Military Techs before I start designing, much less cranking out ships. The NPRs may have other ideas, but this fleet is still meant to be an end goal for my "standard" fleet.

Now this is the re-designed Javelin-Class, fulfilling the exact same roles as the OP, but at half the weight allowing for them to be crammed into any ship with a single Boat Bay:

[Bear in mind the higher tech, there is no tech at or below a cost of 40,000 RP that I do not have access to.]

Javelin-Class Starfighter    250 tons     2 Crew     72.1 BP      TCS 5  TH 50  EM 0
10000 km/s     Armour 2-3     Shields 0-0     Sensors 2/2/0/0     Damage Control Rating 0     PPV 1.4
Maint Life 9.97 Years     MSP 18    AFR 5%    IFR 0.1%    1YR 0    5YR 5    Max Repair 25 MSP
Intended Deployment Time: 0.25 months    Spare Berths 5   
Magazine 6   

Javelin Mk. II Internal Fusion Drive (1)    Power 50    Fuel Use 391.33%    Signature 50    Exp 25%
Fuel Capacity 50,000 Litres    Range 9.2 billion km   (10 days at full power)

Javelin Mk. II Gauss Cannon (1)    Range 20,000km     TS: 10000 km/s     Power 0-0     RM 2    ROF 5        1 1 0 0 0 0 0 0 0 0
Javelin Mk. II B-FCS (1)    Max Range: 20,000 km   TS: 10000 km/s     50 0 0 0 0 0 0 0 0 0

Javelin Mk. II Box Launcher (2)    Missile Size 3    Hangar Reload 22.5 minutes    MF Reload 3.7 hours
Javelin Mk. II R50 MFCS (1)     Range 13.7m km    Resolution 50
Raptor ASM (2)  Speed: 40,000 km/s   End: 5.7m    Range: 13.6m km   WH: 8    Size: 3    TH: 520/312/156

Javelin Mk. II R50 TSAA Module (1)     GPS 180     Range 4.6m km    Resolution 50
Javelin Mk. II R1 TSAA Module (1)     GPS 8     Range 1.3m km    MCR 141k km    Resolution 1
Javelin Mk. II TH Detection Sensor (1)     Sensitivity 2     Detect Sig Strength 1000:  2m km
Javelin Mk. II EM Detection Sensor (1)     Sensitivity 2.2     Detect Sig Strength 1000:  2.2m km

Missile to hit chances are vs targets moving at 3000 km/s, 5000 km/s and 10,000 km/s

This design is classed as a Fighter for production, combat and maintenance purposes
And this is the Javelin II-Class, built to fit the "multi-role" design. I have a plethora of fighters within this fleet each performing a different role, and the Javelin II fits all of those adequately, while not over-lapping with them due to one thing or another. Examples: The Rapier-Class is objectively superior to the Javelin II-Class in nearly every respect, but it costs more than 150% as much in BP to produce and it's missiles cost more than 3x as much as the Javelin II's own missiles while taking longer to reload. [45 minutes versus two and a half! ] The Fox-Class Scout goes twice as fast while massing a quarter of the Javelin-II's weight [thus fitting inside of a single Small Boat Bay] and can shuttle two teams, but is devoid of armament and thus unfit for being pressed into the combat role. The Albatross-Class is in most respects comparable and in many ways better than the Javelin II, but lacks the passive sensor capabilities of the Javelin II as well as the ability to conduct Orbital Bombardment on account of it being armed with only a single 10cm Meson Cannon. As such the Javelin II-Class fits the bill of a "true" multi-role fighter in that it is very the essence of compromise. When in doubt, "Launch the Javelins!"

Javelin II-Class Multi-Role Starfighter    500 tons     5 Crew     156 BP      TCS 10  TH 45  EM 30
6000 km/s     Armour 3-5     Shields 1-300     Sensors 2/2/0/0     Damage Control Rating 0     PPV 4
Maint Life 0 Years     MSP 0    AFR 100%    IFR 1.4%    1YR 8    5YR 124    Max Repair 37.5 MSP
Intended Deployment Time: 0.25 months    Spare Berths 2   
Magazine 6   

StarTech Systems J3M1 Javelin III Fusion Jet Starship Drive (1)    Power 60    Fuel Use 617.3%    Signature 45    Exp 30%
Fuel Capacity 80,000 Litres    Range 4.7 billion km   (8 days at full power)
Javelin Defense Screen (1)   Total Fuel Cost  4 Litres per hour  (96 per day)

Javelin Gauss Cannon (1)    Range 20,000km     TS: 6250 km/s     Power 0-0     RM 2    ROF 5        1 1 0 0 0 0 0 0 0 0
Confederate NaviTech "Javelin" BFCS (1)    Max Range: 24,000 km   TS: 6000 km/s     58 17 0 0 0 0 0 0 0 0

Raptor Missile Launcher (2)    Missile Size 3    Rate of Fire 150
Raptor R50 Integrated MFCS (1)     Range 13.7m km    Resolution 50
Raptor R1 Integrated MFCS (1)     Range 3.9m km    Resolution 1
Raptor ASM (2)  Speed: 40,000 km/s   End: 5.7m    Range: 13.6m km   WH: 8    Size: 3    TH: 520/312/156

Confederate NaviTech "Javelin TASS Module R100 (1)     GPS 720     Range 13.0m km    Resolution 100
Confederate NaviTech "Javelin TASS Module R1 (1)     GPS 8     Range 1.3m km    MCR 141k km    Resolution 1
Confederate NaviTech "Javelin" Passive Surveillance Module [TH] (1)     Sensitivity 2     Detect Sig Strength 1000:  2m km
Confederate NaviTech "Javelin" Passive Surveillance Module [EM] (1)     Sensitivity 2.2     Detect Sig Strength 1000:  2.2m km

Missile to hit chances are vs targets moving at 3000 km/s, 5000 km/s and 10,000 km/s

This design is classed as a Fighter for production, combat and maintenance purposes

@ Father Tim

That is... entirely possible.  I may do that in the future.

The only defense against mesons is to kill them from beyond the range the mesons have, and/or to be faster than the mesons.  Trying to build to duel inside the mesons range ensures you will take a lot of damage even if you win.  I prefer designs that if I manage to choose the range, I win decisively with little casualties.

I've built slower fighters at higher tech, and liked them just fine.
The problem is that this one seems to do nothing well.

It doesn't excel at being hard to spot (capability could be split between several smaller fighters). It doesn't make good use of fighter BFCs (slow, no turret). It doesn't excel at being expendable because it's quite expensive for its capability, and also requires logistics support by a mothership.

Additional capability should be reviewed with an eye to whether it's worth the design concessions. There is always an opportunity cost in fighters - inefficient propulsion plants because we don't have the space, cost and sensor footprint.
Want to add the ability to destroy undefended targets of opportunity, or at least force a reaction, to a scout fighter? By all means add a tiny Gauss cannon even if it's weak per ton. But we should be extra-stingy, a true combat craft isn't in the cards. Smallest version, definitely no armoured mount.  If you absolutely need to add a non-box launcher... how about a magazine for some sensor buoys instead of a second tube? This adds important capability to the recon role if your fighter has no loiter time, and allows multiple pot shots if you go for a combat load and the opportunity presents itself. But not too many optional things at once.

That thing will get munched up in a dogfight and doesn't have the range or speed to fight capital ships. It'll get outrun by capitals two tech levels down and its missiles won't be able to even begin to outrange anything on your tech level. Multipurpose fighters, with some exceptions, are generally speaking a bad proposition as it completely nullifies their advantages over larger ships.