Hey there Viaduk04,
Thanks for reaching out to Apple Support Communities. We understand iCloud Photos folder and shortcuts are being duplicated unexpectedly. We’ll be happy to help with this.
Before you do any further troubleshooting, make sure you backup your iCloud Photos so that no data is lost. We know how important our photos can be and we want to make sure nothing happens to yours while troubleshooting:
Archive or make copies of the information you store in iCloud
After you do that, remove iCloud for Windows once more using the steps under “Turn off or uninstall iCloud for Windows” in this link:
Set up and use iCloud for Windows
Backup your iTunes library after this:
Back up and restore your iTunes library on your PC
Then remove iTunes and it’s components in the exact order listed in this article:
Remove and reinstall iTunes and related software components for Windows 7 and later
Check for any updates to Windows after this and restart your computer. See if you can remove the folders after this.
If not, reinstall iTunes and then iCloud for Windows. You can find info on installing both in the above links. Try removing the folders once more after this and see if the issue is resolved.
We hope this helps.
Take care.