As a user, the most frustrating thing about the unwanted notifications is that sometimes, on poorly or irresponsibly written plugins, they persist even after I close them. Those times I would love a "Mark as spam" functionality, but that would be too much and it could easily be misused, ending up making things even worse.

A less aggressive and maybe more realistic approach would be some sort of "Mute this plugin" option: Users could disallow specific plugins from displaying notifications overall, either permanently or until their next update (in case they indeed need to announce something actually important).