The problem is that I don't know what to do to fix it
I don't really know what cause the issue in the first place.
Maybe doing some structural changes in the database could help, but it takes time which I don't really have for the moment (probably a little more at the end of the month).
The quickest thing I could try would be to return an error 429 to the bots on times when the site is the slower, to see if it helps, as it seems to be the recommended solution, at least for Google).
Maybe I could try restarting the server, in the past it used to help but I'm not sure it will really do it this time, as the last restart was not that long ago.