ECM and ECCM in the early game are really only important for kiting beam ships, who need an absolute range advantage. With missile ships, you can just oversize your fire controls, and it is generally easier to just oversize your fire controls by 10% than to have an ECCM.
As an RP matter, I don't have a problem with building your fleet to be able to travel at a unified speed the length of your empire, but I don't think you should have all your ships built that way.
One of my early fleet experiments was with missile ships with commercial engines and hangars. The fleet theory was to use commercial jump tenders to get around. My survey fleet was supported by commercial jump engines that also acted as mobile refueling nodes. Subsequent games I switched to military jump engines, because I determined that commercial engined grav survey ships were simply not as efficient. Small military ships have much better maintenance endurance than commercial engined large ones. Also, while a geosurvey ship can't really expect to do its job and avoid detection, a grav survey ship might, so commercial engined geosurvey and military engine grav survey made sense to me.
What frustrated me about the commercial engined missile ships was the large number of maintenance facilities I needed. It it very harder to station such a ship for a long time on the frontier.
So my latest game, I have a large number of empty box carriers of various sizes. No engines, just a sacrificial .1 HS sensor to appease the maintenance gods, and they can easily last 20 years without maintenance parts resupply. So I can tow them to a colony world, and station sensor fighters and a small combat wing, and I won't have to worry about maintenance for them.
But if you have an aesthetic that capital ships should be able to operate solo, or with minimal support, and don't mind a little inefficiency, go with the aesthetic.
I myself am a big fan of railgun fighters for PD early in the game. Because the enemy generally can't even SEE the railgun fighters at the range that they open fire, you don't have to worry about your point defense degrading over the course of the fight. They can also be a pursuit wing, going after empty enemy missile ships after your own missile ships take out their beam warships, and thereby save you from having to kill everything in the enemy fleet with expensive missiles.
The ratio of missile launcher to magazine isn't bad. I would go with significantly more magazine space myself.
As far as your missile boats, I note that even your really small ships have a boat bay. Nice for RP, but maybe a little excessive. My early missile boats are 1,000 tons, and there are a number of in game advantages for that. First, smaller missile boats are harder for the enemy to detect. And 1,000 ton shipyards can be retooled VERY quickly, allowing you to keep your missile boat fleet up to date. You can always redesign them with a fire control customized to a particular enemy. And since the missile boat concept is to strike and return to reload, it should not be limited to fleet speeds. It should have boosted engines, and a significantly shorter range than your more conventional warships.
Now, there is something to be said for having your capital missile ships all have a hangar. You can then have most of your scouting element based in those hangars, giving you small, fast, hard to detect scouts integrated into your fleet. Instead of having to refit your ships with new sensors, all you have to do is send them with updated fighters with the new sensors, and retire the old scout fighters to colony defense somewhere.
