What about pods for bomber type ships? As in... EMP pod. Mine layer pod. Etc. ??? They take up a munitions space.

not a bad idea

Crew pod. Adds a crew slot. Punisher crew.

This is essentially what Unguided Rockets is.

Swaps 2 missile slots for a Hydra rocket pod and turns your Bomber/Punisher into an Apache.

Make pods only for ships that have missle / torpedoes. ???

Mine layer pod. Deploy or destroy bombs/mines

which munition space? Or should you do something like a dual missile/torp space much like the boarding upgrades in Armada?

I like the idea of missile pods. It's in the same vein as those used on the AH-64 Apache.
A Missile Upgrade with a built-in Extra Munitions, but both missiles are fired in a single attack.