In older versions of Shotcut, when Settings > Clear Recent on Exit was enabled, it would remove items in both the Recent panel and Recent Projects
Version 24.10 release notes.
Now in 24.10 the ones in Projects are not removed.
Also, after manually removing all the items in Projects they come back after Shotcut is relaunched.
Is it a bug or was it intentional?
It is a bug, but manual removal of one project works for me. I have not yet tested manually removing them all. The workaround is Settings > App Data Directory > Show followed by File > Exit and then delete file recent.ini.
I have a second thought about this now. The menu item says “Recent,” but the list you refer to is no longer “Recent Projects”. It is simply “Projects,” separate from Recent.
How about having the choice between Remove and Remove All when we right-click an item in Projects?
Or Remove Selected and Remove All (restart needed) ?
That would be nice, but that’s not a big issue if it stays as it is. Your workaround is good enough for me 
This is fixed for the next version 25.01: “Recent” in this action implies Projects as well.