When I created a new mod directory a few years ago I tried to remove as many of the original Starwars .xmls from the GameObjectFiles.xml as possible.
Also I removed HardPoints.xml, CIN_HardPoints.xml and HardPoints_Underworld.xml
Did all of that because I thought
if the game has less Xmls to load that will definitely speed up my mod..
In EAW it will just cause the game to have thousands of additional error masseges (they are invisible and not displayed to the player in any way).
With these files removed my mod needed 210 seconds to load into a new GC,
after adding them back it changed back to something like 120 seconds, which is almost the original speed of the game.
So if you think your mod became slow, try to re add these files.
Now if we do a total conversion mod I guess the best way to get rid of vanilla units is either raplacing them by own units using their ingame name or setting the <build_tab_space_units> and <build_tab_ground_units> to "no" or <TechLevel> to 99, in a copy of the original files that is included in the mod.
I have successfully removed all the vanilla hardpoint files from TPC - you just have to delete all the references to them (in the unit code).
Deleting units is more difficult as it will break the AI scripts if you aren't careful. You'd need to keep stub placeholders (an xml entry with basically no code in it) or dig trough all the scripts and update them accordingly. For TPC I went with the former.
Btw, setting <build_tab_ground_units> to no will not disable the unit for the AI.