1) Slow for Ion Ship, 2k kms is more in line with two techs earlier in my experience. That said, missile platforms can afford to be slower to a point, but notice the missile to hit chances, one REALLY doesn't want to be below the first number, and ideally is close to the middle number.
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5) Range is massive for a "coastal defence" platform as well.
It is extremely slow, although for a system/colony defense ship that is mostly meant to hang out in orbit I guess it could work. The bigger problem here is that not only is the ship so slow with boosted engines, but the ship has two size-20 engines (total size 40) but over 50 HS of fuel?! This is
extremely wasteful! First, there is a mathematical rule for propulsion systems in Aurora: the most tonnage-efficient configuration has a 3:1 ratio of engine size to fuel size. Increasing the engines relative to fuel size is often a good idea since it reduces the total cost and amount of fuel needed, but it is almost
never a good idea to exceed the fuel side of this ratio, as it only increases the costs (engine cost for a fixed speed remains constant, fuel cost increases) and increases the tonnage used, there is no gain from doing this. Having
more fuel mass than engine mass is especially, egregiously terrible.
I would recommend to (1) not use boosted engines recklessly - unless you have a good, clear purpose for doing so, it is better to stick to basic 100%-efficiency military engines as your default; (2) don't add more fuel than needed - why should a slow system defense ship need 57 billion km of range? If you need to deploy so far away, just support the ship with a tanker to reach its destination; and (3) adhere to much larger ratios of engines to fuel, 3:1 should be the absolute minimum and I would say most designs for large warships should aim for higher ratios like 10:1, 15:1, even 20:1 depending on what is needed, it is fine to build a "less efficient" ship in terms of tonnage if that means it is cheaper to build and maintain (and refuel!).
2) Deployment time is almost a third of maintainance life, in general I find 150% of max repair fine for "coastal defence" platforms.
This depends. I often end up with ratios in the 3:1 region since I will use Engineering Spaces to reach a desired maintenance lifetime and then add some MSP bays to repair weapons failures in battles. The final number on the design screen can be misleading in this case since those ships are clearly not meant to be on-station for three years at a time or however long.
3) Deployment time is very long for said "coastal defence" platform. Is it ever actually going to be patrolling Sol for 12 months or is it going to be staged at a facility and sent out as a QRF in response to a threat (or just sit in orbit somewhere and provide PPV)
I agree on this count. Aside from a hardcore commitment to roleplay, sending ships out on patrol patterns is rarely worthwhile as there is not much a patrolling ship can do better than a DSTS placed on a nearby airless rock. Sensor ranges on ships are simply not long enough to have effective coverage. Now, if you plan to deploy this at a jump point then a longer endurance makes sense.
4) A missile platform with no PD? Bold choice Cotton. 
(CIWS really doesn't count as PD, it is a commercial module afterall)
I'd probably not even bother with PD here if I am concerned about an "optimal" ship design. If this ship is meant to be deployed more or less alone to defend a colony (rather than as part of a sizable battle fleet), a bit of PD will not do very much to defend it from a serious opponent and it is probably better to optimize for the pure missile role for shooting down enemy scouts or raiders.
Missile:
1) Warhead strength should optimally be a square number, 1, 2, 4, 9, 16, 25 etc.
In my opinion, this point is vastly overrated. Missile penetration is so poor anyways that optimizing the warhead size is usually not worth it. What matters is getting a large enough number of missiles on-target to deal over 50% of the target's total armor strength in damage, at that point armor penetration doesn't matter as further hits will deal massive internal damage through all of the holes in the target's armor. Thinking "oh, if I have a strength-9 warhead, I might deal a point of internal damage if the target only has 2 layers of armor" is a kind of thinking that doesn't reflect the reality of space combat in 99% of cases (the exception perhaps being anti-fighter/FAC missiles, but these usually have thin armor anyways).
2) MFC and Missile Range should match up, having double range on the MFC is overkill, missiles go 106500 km in a single 5 sec increment, in general going over 30 seconds/6 increments has diminishing returns, in this case MFC of 60m km should suffice.
I usually consider that MFC range should be somewhat longer than missile range, as this allows firing and retreating while keeping a target lock. However, 2x range is excessive even for this purpose, though it can be useful for future-proofing to an extent.
Lastly, I do need to point out the most critical, crippling weakness of the OP ship design:
Omaha class Light Cruiser 15,000 tons
...
Jarvis Ordnance Size 8.00 Missile Launcher (5)
This ship is basically useless. A measly five missiles will struggle to penetrate virtually any point defense screen you could realistically encounter. Even with the 2.2+ changes missile combat still requires large salvo sizes to penetrate enemy defenses, let alone to do respectable damage. How does a 15,000-ton ship only have five guns?!? Especially with such a small and weak engine section?!
I suspect that the problem is here:
Hargreaves & Daniels Active Search Sensor AS158-R60 (1) GPS 38400 Range 158m km Resolution 60
Atkins Electronics EM Sensor EM10-60 (1) Sensitivity 60 Detect Sig Strength 1000: 61.2m km
Atkins Electronics Thermal Sensor TH10-60 (1) Sensitivity 60 Detect Sig Strength 1000: 61.2m km
These sensors are much,
much too large for practical purposes - I am estimating size 40 active sensors and size 10 passives, and this is too much. A system defense ship should be relying on the colony's passive sensors (at equivalent tech levels, a single DSTS is the same as size-50 EM and thermal sensors together) to find targets, while a battle fleet should be using dedicated scouts or sensor vessels of some kind(s). Most ships, and certainly your system defense ships, should be using as much space as they can for weaponry - your active sensors and MFCs should match your missile range, not be 2x or 3x greater as this added range is not only useless but extremely expensive (a mere size 6 active sensor would have over 60 million km range, more than enough to work with your missiles).
I will also note that for anti-ship missiles, it is usually better to use the reduced-size launchers to generate a greater salvo size, in fact for a system defense ship perhaps even using box launchers is the right decision if you will always be right next to a colony you can reload from. If you have 50 missiles, it is usually more effective to deliver all of them to the target at once, than to deliver them in groups of 5 or 10 at a time - the latter are more likely to be contemptuously swatted aside by modest point defenses than to actually damage anything.
