IIRC, TUV states that about half the size of a vehicle is taken up by "equipment." That leaves about half the space for passengers and cargo. I think that is probably as formal a rule as you will ever get based on equipment size and volume. As a GM you will just have to decide if it is possible to put a larger weapon or other system into the ship, and how much passenger/cargo space will be lost because of it. Having "encumbrance" information on all the equipment would have been helpful though. I guess that would have been a little too Star Fleet for the game.
Monolith, the Living Titan
"The HERO System is not designed to represent real life. The game is designed to represent heroic fiction as presented in comics, novels, television, and movies."
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