Files on my desktop seem to set themselves as hidden files (macOS Catalina), greyed out, even though they don't begin with periods
We resolved it in the comments as following:


Give full disk access to Terminal in System Preferences > Privacy &amp; Security.
Run

cd ~/Desktop
chflags -R nohidden ./
killall Finder


The -R flag will unhide recursively everything under the ./ (current directory). 
To hide something back, for example:

chflags hidden ~/Desktop/project/.git


Don't use -R here since git only keeps the top level folder, .git hidden, rest all inside it is normal.