No (publicly advertised) per-org limit per se, but one could run into limits due to capacity issues: Question about machine limits and creation - #2 by JP_Phillips
You can opt to delete them, but subsequent starts of the machines (using the same image) won’t be as quick. As of today, Fly doesn’t charge for stopped machines, but that might change. The indication back then was, Fly would charge for the disk space consumed by the stopped machine’s docker image (to the tune of $0.15/GB-month).