Far as number/size of ships go, the one I'm currently designing is a combination. It's a 300m-long cruiser that has a hangar deck for 8 fighters. Also has 4 cargo tugs/tenders (It's a LASH-type in terms of bulk cargo, carries it in barges/containers), and two "rider" gunboats with a crew of ~3-4. Cargo decks are connected to the hangar deck by a pair of large cargo lifts as well, and could be converted quickly to hold another 20 or so fighters. Also has 44 missile tubes capable of firing torpedoes or single-man drop/boarding pods in dorsal and ventral batteries, so there's that =p
I actually did the initial layout of it based on my naval architecture experience and, as it turns out, working on a spaceship's actually easier because you don't have to worry about things like a waterline and, well, gravity. Ended up leaving me with more leftover space than I frankly know what to do with after designating the engineering spaces, berthing spaces, CIC, flight deck, weapons control stations, missile bay, galley, and med bay. I've got about 15,000 square meters of deck space left over even after throwing in trivial stuff like an exercise room and laundry, giving each room its own auxiliary space for storage, emergency power, and life support. And dividing the entire interior into airtight compartments with internal airlocks. We could probably fit 500 Bay12ers in there quite comfortably, all in a nice compact package. Biggest problem would be finding a job for everybody =p
Also, remember that our strength lies not in our numbers, but in our !!SCIENCE!!. Nobody takes basic tools and figures out how to turn them into weapons of mass destruction as fast or as well as us. I mean, how long did it take after the minecart update for one of us to figure out you could turn it into an artillery piece? I think it was something like 15 minutes, then a day to make a self-loading fully-automatic version =p I can see it now... "Did they just blow up our ship with a LASER GUIDED-REFRIGERATOR!!!??" They won't know what hit them.
*EDIT* As far as hacking goes, it seems that wireless capability is going to be limited. Even if it's there, I'd strongly recommend hard-wiring everything. Getting your wifi password hacked is a lot more serious when the guy who does it can flush your life support system
. Seems like to do some hacking you'd have to board the enemy vessel and physically access their computer. Since boarding has been all but confirmed as a valid tactic, I can imagine this leading to some truly epic battles =D