Hmm, so Dropbox, Adobe Cloud and other cloud sync services are a frequent ingredient in the mix, but not always...
Yes, waiting for Apple to isolate the issue and fix it is the real solution. However, given how rare the problem is, pooling our knowledge in this thread is also useful.
Has anybody else seen cases of spontaneous remission? Seriously, I Installed Transporter Desktop, the problem appeared. I logged out and back in, restarted a couple of times without success, relaunched Finder - which helped for a few seconds, checked Transporter for updates... no solution. Then I deleted Evernote, because I haven't actually used it for at least 2 years, and I'm trying to clean up a bit. Pretty sure that at that point I was still having to access the Applications folder in list view.
Went off and did some other things, found this thread, posted "me too", sent Feedback to Apple, then opened my Applications folder again to see if I still had Onyx installed.
Hey presto, I'm in icon view and all icons are present and accounted for. Accessed the Transporter and flicked a few files around, everything syncing fine, icon view still working ok...
So I went and edited my original post to reflect this change, and went on with my day. I've now been off the network and back on, in and out of a range of apps, the issue has not come back. Anyway, back to work... I'll post if I learn anything more.