Update: I'm still seeing hoppers getting stuck.
Either they wont pull items from a chest or item stream, or they wont pass an item into another inventory. CDPIV reported similar problems.
Oddly, the problem seems to be related to which chunk the hoppers are in. For example, I've got a string of hoppers that spans two adjacent chunks. All the hoppers in the problem chunk are stuck whereas the hoppers in the adjoining chunk all work fine.
I've been able to fix the stuck hoppers with a remove & replace. This seems to do a good job fixing them even when I TP to and from the area. Also I've found I don't even need to replace all the stuck ones. Turns out that replacing a just a few of them, or none, and then TPing out and back fixes them!
It looks like after the server restart they get stuck again though.