Is there any way to delete the hotspot files so that they dont re-appear after reboot?

disable hotspot first maybe ?

Apparently not.

I experimented with hotspot a few months ago, but never actually did anything with it. When I turned it on, all the hotspot files appeared, crufting up the output of /file print. I finally decided to get rid of the noise, so I disabled hotspot in /system package and rebooted. I expected the files to disappear, but they didn't.

If I delete the files manually, is that going to screw up any possible future use of hotspot on this router?

Disable Hotspot, then delete the folders. That's expected behavior. Next time you enable a hotspot and the files aren't there the default HTML will get recreated. If you customized it you may want to save it off first.