Hidden mount weapons can't be disabled by EMP or battle damage, that makes them stronger than other types of mounts. Also most missiles weapons don't have:
"renderHints":[RENDER_LOADED_MISSILES_UNLESS_HIDDEN],
and loaded missile appear on top of the ship.
It's less a problem for buit-in weapons as you can balance your ship accordingly, but the best would probably be to make a different phase lance for your ship with no sprite assigned, even if it has the same stats, and flag it as "SYSTEM" to prevent it from spawning in markets and cluttering the codex.