Before I switch to running pifed I noticed that lemmy would still show posts, at least to me as an admin, that where removed elsewhere. It's not a problem unique to federated things, nothing says anything you delete on a central platform is actually gone either, but federated systems are even more impossible to properly remove things from since any given node could store copies.
So yeah, throwaway accounts if you don't want it associated is the way to go.
Depends a lot on budget, space, and electricity costs. Going to 'overkill' level once can save a lot of these issues down the line.
Mine started similarly, some small box with a couple drives that got up sized and then moved to another to add more...
Eventually I bought a used 2U box with 14 bays and set it up with a ZFS pool all made up of mirrored disk pairs and auto snapshots so it can have a drive fail without issue and go back 2 weeks if something gets oops deleted.
Downside, now the whole lab uses about 700 watts continually so the power bill is kinda nuts.