You need to do a little more reasearch by the looks of it. If you want to use missiles against them then go for short range missiles that do 9 points of damage each. That gives 1 point of internal damage per hit, and by the third hit there is almost no armour left if they only have 2 layers. You can put in .01 msp for the fuel which will only give it a .5-1 million km range. everything else goes to engine/agility to up your chance of hitting. If you want to go the FAC route, you might look into reasearching up a couple of levels of lasers instead of the torpedo's. A 15cm laser at close range should burn right through 2 points of armour and it will have considerably more range than the mesons do. A near uv laser with capaciter 3 shoots every 10 seconds and has a range of 180,000 km. That's three times the range of those meson armed FAC. You should be able to make your FAC smaller which will also give you a better chance to hit them while upping your speed at the same time. If you can hold thier overtake down to 2000 km/s then that would give you 5 shots before they even get into range of your FAC's.
If you really want to go the torpedo route, then I would suggest getting your torpedo size up to a damage 4 as that will at least get into the second layer of armour, which means that fewer hits will start to get internals. Currently a 3 point damage torp requires that you hit it at least 3 times in the same area to get any internals. By upping the damage to 4 points it only takes a minimum of 2 hits, by the third hit there should be enough overlap to get something through.
FYI the armour on those FAC's is 2x8. The damage pattern of torpedo's and missiles is about the same. A 4 point damage does 3 to the first row of armour and 1 in the center to the next row. A 3 point damage is just 3 to the first row of armour. The chances of getting 3 hits that all overlap a single point on that armour is fairly low. The chances that 2 hits will overlap is actually quite good, and the 3rd hit from a 4 point damage weapon will get through if it hits anywhere that either of the other shots hit. A three point damage pattern however requires that they have 3 points from different weapons all hitting the same column. You can see why the 4 point weapon has a lot better penetration chance overall.
Another trick you can play is to lay a mine field just before they get into range of your ships. Either larger missiles with a good endurance (20+ minutes) that you fire at a way point, or actual captor mines. Bouy's with a month or two endurance, several medium size missiles each with their own active sensors and an active sensor on the bouy. Set the sensors resolution to the FAC's size and use a very small fuel load on the missiles so you can get the best performance out of the missiles. If the captor is set to release the bouy's at 15 seconds of flight time for the missiles then they should have no problem detecting the FAC's and firing on them. This would give you a way to put a large salvo from just a few launchers. Even if each launcher only fires every 5 minutes with a couple of hours of lead time that is a lot of missiles that are going to be waiting for the FAC's when they come in. Below are some samples that I designed based on what I can tell of your tech. They are not perfect I am sure, but they should be reachable designs. If your design did not give me what I wanted I used projects no more than 5000 rp for all of the background tech. Hope it helps.
This is the laser armed FAC, notice how much faster it is and the faster fire control this allows.
Tribal class Fast Attack Craft 1000 tons 114 Crew 195.8 BP TCS 20 TH 60 EM 0
6000 km/s Armour 1-8 Shields 0-0 Sensors 1/1/0/0 Damage Control Rating 0 PPV 4
Annual Failure Rate: 200% IFR: 2.8% Maint Capacity 0 MSP Max Repair 86 MSP Est Time: 0 Years
GB Ion Engine E70 (1) Power 120 Fuel Use 700% Signature 60 Armour 0 Exp 15%
Fuel Capacity 10,000 Litres Range 2.6 billion km (4 days at full power)
15cm C3 Near Ultraviolet Laser (1) Range 180,000km TS: 6000 km/s Power 6-3 RM 3 ROF 10 6 6 6 4 3 3 2 2 2 1
Fire Control S08 96-6000 (1) Max Range: 192,000 km TS: 6000 km/s 95 90 84 79 74 69 64 58 53 48
Gas-Cooled Fast Reactor Technology PB-1 AR-0 (1) Total Power Output 4.5 Armour 0 Exp 5%
Active Search Sensor MR0-R18 (1) GPS 28.8 Range 230k km Resolution 18
This design is classed as a military vessel for maintenance purposes
Here is the design for the mine that I was talking about One of these should at least cripple a FAC if not kill it. The missiles have about a 2/3 chance of hitting
Buoy Size: 30 MSP (1.5 HS) Armour: 0
Reactor Endurance: 4.5 months
Active Sensor Strength: 0.8 Resolution: 18 Maximum Range: 144,000 km
Cost Per Buoy: 28.004
Second Stage: Size 4 Anti-ship Missile x7
Second Stage Separation Range: 150,000 km
Materials Required: 7x Tritanium 0.9x Boronide 4.104x Uridium 18.72x Gallicite
Development Cost for Project: 2800RP
The missile that it fires is here
Missile Size: 4 MSP (0.2 HS) Warhead: 4 Armour: 0 Manoeuvre Rating: 20
Speed: 30000 km/s Endurance: 0 minutes Range: 0.7m km
Active Sensor Strength: 0.472 Resolution: 18 Maximum Range: 84,960 km
Cost Per Missile: 3.722
Chance to Hit: 1k km/s 600% 3k km/s 200% 5k km/s 120% 10k km/s 60%
Materials Required: 1x Tritanium 0.472x Uridium 2.71x Gallicite Fuel x25
Development Cost for Project: 372RP
And the ship to lay the mines A couple of these with a magazine ship to replentish them can lay a lot of mines in a couple of days. Each ship can lay 24 mines in 1 hour so just two of them with a single day of laying mines with their engines turned down for 1 day can lay 1152 mines. You probably won't need that many. For 200 FAC's I would use two groups, One of 200 mines and the second of 100 mines placed about 1 minute flight time apart. That would take 1 ship only 12.5 hours to emplace. When you want to lure the FAC's to you have a ship with a really big active sensor turn it on. Even a small sensor that has a resolution 500 can be detected very far away - see the big active sensor on this ship.
Victory class Cruiser 7500 tons 901 Crew 1067.6 BP TCS 150 TH 180 EM 0
2400 km/s Armour 1-34 Shields 0-0 Sensors 1/1/0/0 Damage Control Rating 4 PPV 60
Annual Failure Rate: 112% IFR: 1.6% Maint Capacity 356 MSP Max Repair 180 MSP Est Time: 1.38 Years
Magazine 724
Ion Engine E7 (6) Power 60 Fuel Use 70% Signature 30 Armour 0 Exp 5%
Fuel Capacity 150,000 Litres Range 51.4 billion km (248 days at full power)
Size 30 Missile Launcher (2) Missile Size 30 Rate of Fire 300
Missile Fire Control FC3-R18 (1) Range 3.5m km Resolution 18
Size 4 Anti-ship Missile (1) Speed: 30,000 km/s End: 0.4m Range: 0.7m km WH: 4 Size: 4 TH: 200 / 120 / 60
Size 30 Mine (24) Speed: 0 km/s End: 135d Range: 0.1m km WH: 0 Size: 30 TH: 0 / 0 / 0
Active Search Sensor MR128-R500 (1) GPS 16000 Range 128.0m km Resolution 500
Active Search Sensor MR2-R18 (1) GPS 288 Range 2.3m km Resolution 18