"Hytale’s server technology will be provided shared source, which means that everyone will be able to read the server code. "
The server will be open source which means there could be a different approach to plugins. I think what Hytale expects us todo is to modify the server source so that we integrate code and resources of our own. However there are 100% going to be communities like spigot out there who will make an API where developers can plugin their java sources. I know for sure that I will be creating my own server.jar so I do not have to worry about external java plugins.
Hytale gives developers/owners more freedom by giving you most of the resources like the 3D modelling tools, server sources, assets which is a lot more attractive for community owners.