A while ago I thought I read in the Whonix documentation not to put icons on the desktop or use common directories like ~/downloads, ~/documents, etc.
I tried to find it again today and couldn’t. I’m assuming it’s OK to do those things?
No, the wiki didn’t comment on desktop icons.
Chapter File Storage Location indeed recommends to avoid certain folders.
(Links to Kicksecure wiki, because Whonix is based on Kicksecure.)