Should I delete the cgi-bin folder in a subdomain I just created?

You can safely delete it. "cgi-bin" is hardly ever used these days.

You can safely delete "cgi-bin" folder, it's hardly ever used nowadays

Also beware that when your server got some malware scripts scans different folders and then hides on folders like cgi-bin because they rarely are checked now.

I even wrote a script before that "monitors" different folders in my server and alerts me if it found different scripts in there on my personal and clients servers too.

I haven't seen it mentioned but it might also be worth noting that since cgi-bin is traditionally used to execute scripts, some hosting providers might require you to edit your .htaccess file if you wish to execute scripts outside cgi-bin (same is true if you deleted your cgi-bin).

cgi-bin historically was the only place where executable or script code (binaries, shell scripts, etc.) could be stored. It is mostly a historic relic since most hosts allow execution of scripts from anywhere.