Hello, is it allowed to use a spigot plugin which deletes the worlds with an command? Or does it give any other way to do that without delete the folders everytime?

I'm assuming you are talking about a server...

Although I cannot say this with certainty, I do not think you are allowed to use that spigot plugin. Spigot, Bukkit, and Paper are considered modded, and thus banned for speedruns. If you are using spigot plugins in your server to delete worlds, that must mean that your server itself is spigot.

However, all though I may not be correct by saying this, if you use that plugin to delete the world and then switch your server to vanilla before speedrunning, you may be allowed to do that. I am not 100% sure about this, but all I know for certain is that the server where you speedrun may not be run on Paper, Bukkit, or Spigot.