Really is a drag for my Horse Hide + Human skull perk mod.

Why though?

If the skull is part of an "npc skeleton" meaning that it was either fighting or can be "raised" it cannot be looted. Also if it is missing it's jaw it cannot be looted. As for why...no good reason

Yeah I mean the stand alone skulls, sitting on shelves or as decoration to an environment.

So they do not have jaws? It just seemed like some were lootable some were technically not.

If they lack a jaw they are absolutely unlootable. In the player home on Solstheim there is a display case filled with skulls, out of the many there only 2 lack jaws and only those 2 cannot be taken

Some of the skulls in the game are "static" objects, meaning that you can't interact with them (or pick them up). Bethesda most likely intended the "static" ones to be for decorative purposes.