Sheilds do honestly nothing, You can just ram through them with a MAS and then ram through the hangar sheilds.
What i look for when building a ship:
Weapon systems, Usually a big laser in the front, and some turrets on the sides. Ballturrets guarding the hangar.
Power generator. Thanks meek.
Thick armor
Three layers:
Outer layer: Medium plating. Good enough to hold off a bushmaster ACR, Takes med. damage from rocketlaunchers.
Middle layer: Thick as hell, impossible to penetrate.
Inner layer: More detailed, thin, and easy to peirce.
Lots and lots of interactive peices.
I always have overrides for controlls in my bridge.
IE: A Button to lock the hangar doors, Button to make bars drop down infront of/behind doors to prevent escape and entrance from inside the ship
Something to flood poison gas into vents (Gives a warning to all crewmembers to put on a gasmask of some kind and clear the vents incase technicians are repairing stuff)
One or two support vehicles in the hangar, maybe a sublevel with an elevator to hold more vehicles.
ALLLLLLWAYS an alternate way into the ship. The hangar is okay, but that's just for loading cargo and smaller ships. Usually an entrance dock in the back/front sides is good.
Here's a tip.
Enemies, or at least the stupid ones, are just going to get inside your ship and kill everyone.
Enemies like me are going to send a team into your ship, instead of entering your ship personally.
I always send four men, Two with C4s and machineguns of some kind, One medic, and one engineer.
SMARTER ENEMIES (Including me): They get inside your ship for a purpose. Some want to sabatoge it (Stupid enemies can do this), Some want information, some just want to capture you and turn you into love slaves (Optional)
Also:
Keep more than one type of fighter in your hangars. Four MAS's and some kind of bomber is always good.
Have the MASes defend your bombers while the bombers take out turrets and engines. Then have a squad sneak aboard the ship and accomplish whatever objectives.
I hope this has been useful, if you want any other tips and tricks, Just message me.