I really haven't designed a specified nebula ship, but I would think that it would just be a high armor and thruster ships with the engines being a little more efficient than other military ships.
depending on tech level I often find that the armor is the limiter on ship speeds more than the engines. I you want the ships to work outside of the nebula and keep up with other ships then you end up with your standard level of engines and efficiencies. If not then a more efficient engine, or fewer engines can be a good choice.
I used to play a lot in nebula's and I ended up using a couple of types of combat ships. As missiles and shields don't work in a nebula all long range combat is pretty much eliminated. You need to do a lot of damage really quickly with beam weapons. The weapons that I found worked best were railguns and mesons. The mesons short range is normally irrelevant because of the nebula's effects on fire control. Their ability to inflict internals immediately, and the high rate of fire with light mesons work really well. Railguns on the other hand were heavy hitters to blast through thick armor. Their high rate of fire was useful as well because of the nebula's side effect on accuracy. In your nebula the range is 1/6 normal, so even point blank shots are going to have a fairly good chance of missing. Example, at the 10,000 research point your beam fire control rating is 32,000km. With a x4 range beam fire control in that level 6 nebula that means that 20,000km you only have about a 50% chance of hitting. Almost any weapon you can have is going to be doing its max damage at that short of a range. Assuming equal amount of tech in your weapons this translates to a max damage of: Railguns 5(4 shots however), Lasers 10, Particle beams 5, Plasma Carronades 24(double recharge time however) and Mesons 1. Railguns tend to do about twice the damage of the lasers, and equal damage to the carronades. They hit more often however which tends to do more aggregate damage. Carronades will however do more shock damage which may even things out somewhat. Particle beams are a clear loser in a nebula as they are designed for longer range beam combat. Mesons are the exception to the damage as their damage automatically bypasses armor.
Fighters and gunboats are also very hard to make work as they have to close to very short ranges, and normally putting enough armor on them to get them moving fast enough to survive is a real problem. The best combat ships tend to be either just big enough for the engines/armor/weapons you want, or real monsters which can take advantage of the savings that big ships can give you in armor and the ability to put really big systems on the ship. Big systems with lots of potential hits to kill (htk) are one way of reducing the effects of mesons and shock damage. This works because a large system like a 50 hull space engine has a htk of 25. Anything doing less than 25 points of damage in a single hit may not kill the system. For a meson each individual shot is 1 point of damage and therefore only have a 4% chance of killing the engine each time it is hit. What systems are hit is random, but based on the relative volume they take up. You can see the relative amounts that a particular system takes up on the ship design screen (F5) component summary tab. Design a couple of radically different sized but similar ships (beam destroyer vs. a battleship) to get a feel for what I am talking about.
One thing to remember to check is the ships operating speed. If the ship can move faster than the nebula reduce the task force speed to match the nebula limit. I used to notice this reduced the fuel use. Once you are out of the nebula you will need to remember to change the task force speed however. I haven't run into a nebula in a couple of versions so this may have changed.
