Hi, excuse my ignorance but, using these skin plugins, can they ban your account in any way?

I don't believe so, being as the server is issuing them. I wouldn't abuse it though with paid skins, and the functionality to do this may end should Facepunch decide to restrict it.

So, if I use it on my server and add a few skins from the workshop, nothing would happen, I understand, from what you have explained