I had no problems with the ending of Spirited Away, even though as you said there are unanswered questions of what exactly happened. I think I might just be really annoyed/frustrated by Ashitaka: I wanted to like him, he has good intentions, but he seems incredibly naive and I don't really know what he thinks he's doing. I'm not sure he knows either. That seems like an extremely dangerous approach to take in such delicate situations like the one he finds himself in. Sure, he's young, but iirc he was also a prince so he should have been taught to think about things like this. He seems to act mostly on instinct.
I think I'd feel better about the film if there was an "Ashitaka thinks about things" coda, at least in fic.

I'll have to check out Totoro :)