I add a note in the password manager's notes field for sites where I've added Yubikeys as the second factor. I can get the list of the sites using search, and from time to time I go through them to check if a backup key needs to be registered. I create new accounts infrequently.

Would be nice if you could get an exact clone of a yubikey, so you always have a spare in case you lose one.

Though I think there is also the option that sites can store some sort of identifier on the key, then this would not work:/