At my previous job, we had an entire system aptly named Pandora whose entire role was keeping track of which ssh keys were permitted to be found on servers. It had a bot that would crawl through every server, and if it found a key not in it's database, it nuked it. Every new person or automation key had to first be registered fomarlly, with an end date. A bit of a hassle but definitely necessary for the space the company was in.