It's actually less about whether interior weapons would be too powerful and more about whether they increase or decrease interesting choices when designing ships. For example, right now the player has to make interesting choices between adding weapons, shields, or armor to the outside of their ship, as well as where to place reactors/ammo such that they're close to the weapons without being too vulnerable. Low-powered interior weapons seem like they might actually make ship design less interesting.
So what I'm actually thinking of adding are very large, very expensive super weapons that use a lot of ammo/power and have really long cooldowns. These weapons are very easy to destroy, but can be placed on the inside of ships. Ships are likely to have only a few of these and will still need weapons on the outside, so they shouldn't reduce interesting decisions too much, and may even add interesting decisions (such as, should I surround my super-laser with several layers of armor?). They should also add interesting decisions when attacking a ship that has such interior super-weapons (should I take out the exterior weapons first, which are easier to kill, or go straight for that super-laser deep inside the ship?).
