I use the "hide part" in the designer as design help, to check parts behind others or place stuff there -- I guess that is what the hide function is for? But I assume (never tested) that saving a ship with a "hidden" part does still show this part in the game/battle viewer, so activating "hide" does only work in the designer?
Because I thought it would actually be nice to place components to get the stats up but have them really hidden, so that they do not show up in game anymore.
Why? Well, because I remember the nifty tool in GC2 Ultimate allowed you to easily customize ships styles for all civs, but the AI had the annoying habit to place weapons or other components in absurd places and sizes on your carefully crafted custom designs.
If "hide part" would work in-game in GC3 we could just design ships and set all components the AI would place as "hidden" so they do not mess up the look...