Flagging plugins for updates is probably a good idea. I’ll need to think a bit because some cases may be an updated plugin for a new version. For example the next update of generators will include support for z-matrix coordinates. But that’ll require v2.1 of Avogadro.
I’d probably go for the two levels you mentioned:
- no automated check (current behavior, only show when you open the window)
- some sort of opt-in notification that there are updated plugins to install
I’m pretty reluctant to use automatic updates - in part because I’d hate to break someone’s workflow. 
Oh, everything would be opt-in. As I mentioned elsewhere, there’s a new build for Windows with crash reporting built-in. But IMHO, that won’t be the default build for Windows and you still need to opt-in at startup for it.