This is a vanilla server

Yes, lags like a bitch when you have too many entities.

I understand having it in factions servers

Not that necessary, plugins could be much more selective, also, if anything, it's more necessary for vanilla servers.

It don't think it's necessary.

It is, like really is important, server used to crash on a regular basis when we didn't have it.

Even if it was every 3-5 hours

Our restarts take care of unloading stuck chunks and refreshing the world, the entity clear seems to work best every hour, just enough to stop the server from crashing, not too much to really piss anyone off.

I suggest there is a larger more visible warning maybe 3 lines long and in bold red text

We try to keep messages short and to the point to avoid spamming chat. To me, it's quite visible, it's different from all other messages, it happens once a hour at fixed intervals.

I was working on making it avoid the trading post but that causes side effects, it won't clear anything in the nether or the end if I set coordinates to avoid.

Those crashes were happening about every 2 hours, doing a clear at one hour keeps it under control to the point where it doesn't crash.