To expand on that atmosphere thingy:
Beam weapons, except for Mesons, have their damage reduced when shooting through atmosphere.
0.1 atm will reduce damage by 10%, 0.5 atm will take off 50% of damage and so on up to 1 atm, where no damage at all is dealt.
Also, after reduction, the damage is rounded _down_ which makes damage-1 weapons all but useless even in the thinnest of astmospheres
Mesones are _not_ affected by atmosphere, but are precission weapons, so can only be used to take out PDCs, but are no use vs. ground troops or populations (you would have to shoot every inhabitant on the ground singularly, i.e. one after the other, as there is no area of effect).
Re. your Missile Destroyer:
They are actually pretty fast, given Nuclear Pulse Engines.
I see your newer missiles are now a full size, i.e. no 5.something. This is good, as a fractional sized missiles are an inefficent use of space (you need a size 6 launcher to fire a 5.1 size missile)
Personally, I would probably have reduced the size to 5 for an additional tube and tried to get missile speed up to around 12 or 13k, but that is a very personal thing and your size 6 is fine too. It definitely packs more punch than my regular size-5 ones.
Maintenace time is a bit excessive, with just 1 year of deployment time, you could easily half that (or third it)
Also, if those ships work in groups of 3+, drop the CIWS and put a small Gauss turret on them.
CIWS only protects the ship it is on, while regular PD-turrets protect the entire TG. Yes, turrets are larger but with several ships, the benefit of an interlocking PD system is a quite large.
(A CIWS is roughly half the size of a regular dual PD turret or about the size of a single gun turret, so if 3 ships have a single gun turret, you have three barrels protecting every ship in your TG instead of the CIWS´s two and the more ships in the TG, the better it gets. Of course, you now need a res-1 sensor too, but a rather short ranged will be sufficient and in the long run, you want to employ a layered missile defense, i.e. Anti-missile missiles and PD guns, anyway)