the usual thing that happens is the item is substituted with some Maxis clothing, hair, or accessory (as applicable); it boggles the mind that EA/Maxis didn't think to include a "remove from wardrobe" function.
When you delete clothing, hair, or accessories via Body Shop's CAS or the in-game Create-a-Family the mesh for the item you delete isn't usually deleted since these files are typically separate from the recolours (unlike objects). It's usually safe to leave the meshes since they don't take up much space and it (usually) harms nothing to have them. But if you feel compelled to delete them,
Delphy's Download Organiser is fairly reliable for removing orphaned meshes once you have deleted all the recolours (nota bene, it will register meshes linked to shower-proof skin tones as orphans! so user beware!)