Ultranova EMP Missiles would actually do a small amount of damage and could even start fires (either by overheating parts or just do to the fact it's basically a giant lightning bolt curled up in a glass ball if you go off the game's design of the missile)
Crew cannot carry "batteries" without proper equipment, or they can take damage and/or die.
"Batteries" can only last so long without being stored properly, so long trips of crew carrying "batteries" would just result in an drained "battery"
Batteries would be nothing more than a Glass Jar filled with Reactor runoff.
All Projectile Weapons (Excluding only Ion Beam, Missiles, and Tractor Beam) Would have some kind of shell casing, Such as:
Ammo Weapons would have shell-casings, Railguns as well. Energy Weapons would have glass containers.
Thus crew would need to carry off the shell casings to maximize efficiency.