I looked at the list of them in the guide and see a few I've never encountered or encountered a path that would obviously lead to them. I'm guessing they are, per Troika tradition, not fully implemented? 7, 8, 28 from a quick skim.
Some repuations (NC at least) are contradictory or occur in lieu of other reputations, so no, you can't acquire all of them.
Not what I meant (as the post itself makes clear). Are they all actually obtainable in game=are there no unused ones.
Well let me step aside then, big stuff. Yes, they are all obtainable except a few custom ones by Sitra Achara in the mid-range that haven't been implemented yet and may never be (29, 30, 31, 32). Also 40 was somehow never entered, but we'll change that. (Did no one ever notice that they didn't get a rep for (lawfully) killing the slavers?)
I just killed the slavers. No rep. Also, as the game does not end after killing Zuggtmoy now, could there be a reputation like "Demoness Banisher" or something? She's like the biggest force of evil there is, a focus of the ToEE, and if your group of adventurers defeats her there should be some sort of recognization for it.