Does Opera Mail put anything in the registry
Yes.
if so, will that be cleaned up by the uninstall?
Some stuff will be. Stuff that remains shouldn't be a problem.
Been playing around with Opera Mail, testing some import scenarios.
Just delete "C:\Users\John\AppData\Local\Opera Mail\Opera Mail\mail" (and optionally contacts.adr, wand,dat and operaprefs.ini in "C:\Users\John\AppData\Roaming\Opera Mail\Opera Mail" while Opera is closed. When Opera Mail starts up, you'll get the import dialog. That's all you need to do really. You don't even need to uninstall Opera Mail and reinstall it (unless you want to fix Opera Mail registry settings). And, when the import dialog pops up this time, if you have Opera 12.16 installed to "C:\Program Files (x86)\Opera" and it's the default browser, you'll get a new import option that copies the whole mail folder, contacts.adr, wand.dat and operaprefs.ini from 12.16 over to Opera Mail so that all your mail and settings are restored.
Am I missing anything?
You got the idea just fine. Although, it's a little overkill for what you're trying to accomplish. But, it'll do the trick just fine.
C:\Users\John\AppData\Local\Opera Mail
C:\Users\John\AppData\Roaming\Opera Mail
Note that those "Opera Mail" folders contain a folder for each Opera Mail you have installed. For example, if you have "C:\Program Files (x86)\Another Opera Mail", you'll have "C:\Users\John\AppData\Local\Opera Mail\Another Opera Mail" and "C:\Users\John\AppData\Roaming\Opera Mail\Another Opera Mail" folders. As you can see, the names of the profile folders in those Opera Mail folders are based of of the program files folder names. So, really, you only need to delete "C:\Users\John\AppData\Local\Opera Mail\Opera Mail" and "C:\Users\John\AppData\Roaming\Opera Mail\Opera Mail" if you want to clear the profile for "C\Program Files (x86)\Opera Mail".