Pretty great mod. Even before I discovered this I always challenged myself to make the smallest yet combat effective ships I could in vanilla.
Honestly though I really think the shields could use an improvement. The arc and bubble shields currently in the mod don't really feel "complete". Perhaps maybe two larger sizes (2x2 and maybe 3x3) could help.
Same goes for the larger roof weapons (the roof cannons to be precise). Indeed, I really like what you did, but I think a laser variant would be nice. Would certainly pave the way for the creation of effective carrier ships.
Final suggestion: Triple cannons! Basically a twin cannon with an extra barrel added. 🙂