Dragons have an innate True Sight. High ranking demons and devils should have, but that's not always the case. So should liches, but i don't think that was implemented in vanilla, at least not consistently. Vampiric mists have an innate ability to detect invisibility, as do Hive Mothers. The Myconids mentioned by the op also see through invisibilty.
Bioware wasn't very consistent with implementing abilities (and alignments). Plus Bioware toned down a lot of creatures (compared to their PnP counterparts) to keep the game playable for newbies. Understandable of course, but the result often was that some opponents were a complete joke compared to their PnP counterparts. Dragons being the prime example. Some mods will actually add to the confusion. Other mods will restore some of the innate abilities. For instance, iirc Tactics restores the True Sight innate ability (as well as some others) to Pit Fiends.