I assume so - after all, the descr_sm_faction file or whatever it is that says "this faction is that shadow" is the same no matter what campaign type you select. Besides, short-campaign target factions are set as they are because they're the most likely/easy/immediate road to expansion for your own and it's a safe bet you'll be wanting to run them through first in a long campaign as well, so I really don't see why a dev. would disable them.