[Alneyan]

I believe bases count; it would make sense if nothing else, as otherwise you could have two thousand bases to fight against two hundred ships. Don't quote me on that though, since I scrapped all my bases in a 200-ships game.

Mothballed ships/bases do not count against the ship limit (or ships being built for this matter). And they aren't counted in the score indeed, so you never know if your foe has mothballed ships, and how many of them.