Right now my biggest doubt is whether a 3000 ton beam ship with a single 50cm plasma carronade that deals whooping 64 damage at point-blank but only fires once every 55 seconds is worse or better for a brawler than 4 15cm carronades that fire every 5 seconds thanks to capacitor recharge rate 6 and deal 6 damage each for a total of 24. I have proposed designs for both approaches here, with no shipyard tooled for either yet, and I'd like to ask your thoughts. While the bigger one can still deal damage at much longer ranges, the crippling damage attenuation makes such benefit dubious at best, useless at worst. To maximize plasma the optimal distance must be <= 10,000 km, which also requires ships that won't be blown to pieces instantly and preferably faster than the average for their given engine tech.
Maybe save the big guns for the 13,000 ton designs that will happen in the future, once a shipyard expansion is over, which will take a while due to 2 slipways.
First of all, the words "3000 ton beam ship" and "brawler" do not belong in the same sentence together. A 3,000-ton ship can have many viable uses, and if I'm being honest putting plasma cannons on such small ships is a viable way to construct an "emergency" JP defense fleet. However, for a general-purpose beam brawler you really need a heavier ship that can mount enough armor to close the range and actually survive a beam brawl - plus enough engines, fuel, good BFCs, etc. to have a capable ship.
In this case there is no question in my mind that you should be planning on a much larger ship. 50cm carronades cost 30k RP, which is a sufficiently advanced tech level that you should easily have slipways of sufficient size in your empire to build ships of a useful size (compare to ion engine tech, which is a common start-of-game tech level for many players and this costs 10k RP plus the preceding techs).
That being said, we must make do with what we have available:
The major advantage of building small ships, and I must concede that there is an advantage, is that you can build a lot of them fairly quickly. So to assess these designs we really want to think about a fairly numerous swarm of them and not just assessing a single ship at a time. Given this, I think the optimal plan is to build both ships in roughly equal proportions. The 50cm variant provides a heavy alpha strike which can eliminate key targets in the first salvo, or at least damage/cripple them - even with the poor penetration profile of plasma weapons, 64 damage will chew through a lot of armor and deal internal damage to many NPR ships, not to mention the potential for a lot of shock damage as well. The 15cm variant provides the necessary DPS to clean up after the first volley, either to eliminate damaged ships before they can fire back again or to press the attack against surviving ships.
Note that you should be able to build both variants out of a single shipyard, so tooling for two classes is not a problem here.
As general advice, I recommend
not using thermal reduction on your engines for the most part. Most ships do not need this for their mission, and particularly not small ships which are not intended for stealth missions. Conversely, thermal reduction makes engines very expensive, so ships will take longer to build and will require much more gallicite which is often a scarce resource.
Here they are, and the jump scout will likely be used to squadron jump the beam frigates into potentially hostile territory while remaining behind:
This doesn't work, a squadron jump always requires the jump ship leading the squadron to jump through with its squadron. Only a standard jump can leave the jump ship behind.
A modular survey ship questionably defined as scout carrier with a 375tons capacity hangar and a reduced heat signature engine, that houses a "fighter" without engines or fuel and a single grav or geosurvey module so the same vessel can swap survey roles by swapping its "fighters" and pack the bonus of never suffering maintenance failure on the survey modules which is quite expensive in MSP.
This is a really cool concept, which sounds like absolute micromanagement hell to execute in practice. Also note that you aren't saving anything in MSP as the ship with the hangar must pay to maintain its parasite. Also, the bonus from the Science officer is not passed to the parasite survey satellite, just FYI.
Is there something wrong with the Jump Scout+ELINT or does it have to get dangerously close to an alien contact and keep that position for a long time to get anything out of it?
It should work fine, but it's useless tonnage if you expect to use this ship for squadron jumps as in that case you want armor for surviving or some weapon to contribute to the battle.