Try a -5 or -10 penalty (so it's hard to hit but you might easily do half damage)
Character scale, in generall no area of effect weapon target multiple starship cale squares unless the opposite is explicitly stated.
To my experience there isn't, since the size of a starship scale square varies (arguably due to terrain/obstacles). but there are rnage conversions for different weapons between the two scales (in the core book and in clone wars)
edit:
I would disagree about the "completely" part, I would certainly allow smaller friendly ships to occupy/traverse those squares and possibly do the same for bigger/same size friendly ships. (that is unless I missunderstod you)