Now let me start with the science vessel. It's not a bad ship. There are still a few things which in my opinion could be done better but it's not bad. My suggestions would be:
- I would put 2 geological and gravitational sensors on board. A ship like this will pass a lot of time standing still and prospecting/surveying. Multiplying by 2 the sensors means cutting that time in half
- You could probably lower fuel and engineering bays a bit. The ship has a planned deployment time of 4 years, quite a bit of that she will be not moving and prospecting /surveying instead
- I question the utility of the active sensors on this kind of ship. Keep in mind, using an active sensor is kind of like lighting a fire and shouting "hey I'm here". Not the best approach for an unarmed, science vessel ship. Passive sensors instead are good, perfectly fit for this kind of ship. Stealthied engine is also good. You can also cut down armor a bit for more speed, but that's optional.
Regarding the destroyer I see a few problems.
- The biggest one is that you do not have a resolution 1 active sensor. Without a resolution 1 active sensor you will NOT see incoming missiles! And so your point defense weapons will not shoot. Remembering the other thread you posted, this is probably why you did not see incoming missiles. And yes, it happened to all of us some time or another
Your warships should have a resolution 1 or similar active sensor for missiles and fighters, and a higher resolution long range sensor for bigger ships (like the one you have).
- You have a single engine. While that is more efficient for fuel, it's more risky. A single lucky hit you take might destroy your only engine leaving the ship dead in space. This is why most people go with multiple, smaller engines for warships. You'll lose some fuel efficiency, but gain in resilience against hits.
- Generally speaking, your anti-missile capabilities are a bit on the low side. 2 AMM launchers and one CIWS. Even in a squadron of four ships, that would not be enough to stop a somewhat serious missile attack.
- The missiles are a bit big. You might wonder why that's a problem, but the bigger the missile, the easier it is to destroy it. You wanted very high chances to hit probably, and also I'm not sure on how high are the technologies involved in that missile. But being so big, it risks getting intercepted quite a lot. Still it could work.... depends on what enemy you face.
- The range is not the best. That's not a problem per se. You just have to keep in mind and keep a tanker available to refuel!
Those are the main points. After that, it's a matter of preference. A valid tactic to increase weapon space on board of ships is to not have a jump drive on every ship. Instead you could use a dedicated "jump tender" ship which moves the ships from star system to star system, and use the freed up space for more weapons, armor and the like. It is a lot less versatile though, so it's a matter of preference.