It's not just items, there's tons of content the devs just don't care if you miss or not. But i love that, it's a big part of the game managing to make such individual adventures for people. Forums and reddit have loads of posts with stories of people who have played hundreds of hours, finding out about something completely new to them.I think I might have that spellcrux amulet, I'm not sure. I definitely freed the dudes from jail in moonrise prison, but I did it a weird way that involved sneaking around a lot so I might have missed an actual fight with the warden. Definitely don't have the pearl of power though. I did Omeluum's quest but didn't know he sold stuff after.
That's another complaint with this game, there are way too many REALLY important permanently missable items in bizarre locations. Like, there's this one hat that gives you +17 to int no matter what your base stats are - that is on some random stupid mob you have one chance to kill in act 1 and then he disappears. There's no other item in the entire game that gives this benefit. Stupid. If the game was only like 30 hours long it would seem less punitive.