That makes sense...
Still, it would be neat to see that accounted for in Newtonian. It wouldn't even have that much overhead as far as I can tell; it can recalculate fuel weight every time it does a maintenance check, and all the other cargo whenever it changes (missiles fired, cargo unloaded)
As for the weight of missile ships changing, that makes sense. Of course, a ship like that should have to compromise; if a significant amount of the ship is made up of missiles, it is probably poorly armored, very slow anyway, or some other compromise.