So small AMM ships and small missile ships are a waste of time in general then? Well then where should my AMM batteries and Gauss/Meson batteries be situated at on the size scale?
The main problem is that your ship has no personal level of defense. There is no armor, meaning that warhead of 4 or larger hitting it at any point is going to fry the heck out of internal systems, and significantly larger means the entire ship can be gutted in one hit. They have no defense in speed, as they are within the targeting band of pretty much any threat you can expect to face. They have almost no defense in redundancy, because they're so darned expensive.
Due to their low deployment time, they make very poor escorts, as well. Probably a good idea to use more engineering spaces, as they're just big enough to be very inconvenient for carrying around in medium-small size carriers.
Now I see why they're so inefficient for their size even in spite of all the prior statements, they use jump drives.
I suggest building an isolated commercial design ship, with the military jump drive on board (military jump drives can be mounted on ships and still be considered commercial ships, yes, and military jump drives jump both commercial and military ships within their size). Make sure the commercial vessel is equal to size in it's jump rating, you can easily do this by filling in all the empty space in the design with fuel storage. Check it off as a tanker, and give it the Hull designation "Jump Tender", and have it accompany any naval task groups you're thinking of taking on invasion journeys, leaving it behind at the jump point for any risky situations.
Now that the jump drive has been removed from your military design, you now have a lot more tonnage space freedom to design your missile ship, at which point you can now add layers of armor, engineering spaces, a somewhat bigger and lower multiplier engine for fuel efficiency, etc. Especially now that you realize that it's probably efficient to make this ship bigger, up to 5,100 tons (if you don't know what else to add: more engineering spaces is usually the best default option to go with.)
Conclusion: Not burdening your military designs with jump drives makes assembling a large army much cheaper, and much more tonnage efficient.
Other than that,
The resolution of the sensor and fire controls should be 1. The magazine is quite small as well. You don't need ECCM, much less two.
is very important as well.