I think both work since opus is the codec but ogg is the container, but personally I’d probably go with .opus because it’s more descriptive.
Btw Apple’s ALAC and AAC files are typically stored in an mp4 container but with the m4a extension to mark it as intended to be audio only (although it may have a video track, which usually is used for album art).
I’m really not sure where I originally read it. I did some digging and I found some discussion about FLAC and patent trolls on a few forums, including the Talk page of the Wikipedia article, but I haven’t found anything concrete.
It might be that the patent troll thing was just a rumor!