What is the max limit of Missile banks on a fighter/ bomber?
I believe it is 3 primaries 4 secondaries, unless the SCP changed it recently.
Is it possible to have more then one eye point per ship ( Capships, not fighters )?
I would like to add a 'turret-cam' 
I don't think it has any effect having more than 1 eye point, I think the game chooses the first it finds and sticks to that one.
A turret cam is only possible through Nuke's IR tracking system I think, so you'll have to go down to the Scripting thing to get help there.
What's the difference between the flags "capital" "supercap" "cruiser" "corvette"?
I mean, what's the difference in AI behavior ?
Which one is the best for a capship with a lot of side mounted turrets?
I think they're all more or less the same now, but in Retail, you could give cruisers and corvettes "attack my target" and "depart" orders while you could give capitals only the "depart" order. Supercaps didn't accept any orders. This was all changed recently though, I think, since in the recent builds I could tell TrashMan's Whitehall installations to kill each other (and everything else in the mission too, by smacking them around).
Ships with the "supercap" flag can only be damaged by weapons with the "supercap" flag.
The effect on the AI is minimal, so you should just go by size. If your ship is 100-500 meters in size, go for cruiser, 700-1500 meters go for corvette, 2000-4000 meters go for capital and 4000+ go for supercap.
(I am not responsible for any problems caused by following my advice)
