You don't have to drag them out one at a time. A Finder search can gather every "… 2" folder from all levels of iCloud Drive into one list:
1. Open iCloud Drive in a Finder window and press Command-F (that searches only inside the window you're in).
2. A row of criteria shows up under the search field. Set it to Name, then "ends with", and type 2.
3. Click the + at the end of that row and set the new one to Kind is Folder.
Before deleting, skim the list in case one of your real folders also ends in 2 ("Year 2" and the like). Press Command-A, Command-click any you want to keep, then drag the rest to the Trash. Nested "2" folders inside another "2" folder just go along with it. Nothing is gone for good, it all sits in the Trash first.
As for why: when iCloud hits a sync conflict, often right after a macOS update, it sometimes keeps a second copy and adds a 2 instead of merging. I'd wait until iCloud Drive in the sidebar has finished syncing (no progress circle next to it) before cleaning up, otherwise it may bring them back.
— Dmitry · developer of ComfortFiles