That seems to be normal behaviour for Chromium/Blink based browsers.
Google Chrome does the same.
An update generates a new folder with the name of the update version, the previous one is kept, and the one before that is deleted, so you always have the current version and the previous version.
I guess this is so it can be rolled back easily if there is a catastrophic problem found with the new version, although I've never seen this actually happen.
In Opera's case, the shortcuts always point to launcher.exe, which is in the folder above the version folders.
This should never change, although the version of launcher.exe can and does change of course, it's still in the same place after the update, so shortcuts and their associated icons should not be affected.
Why they were in your case is a mystery!