There is currently a limit of 64 gui scenes loaded at the same time (although I think we’re making that value configurable). This should in some sense be an indicator to not go overboard and break everything down into many many tiny gui scenes, but as @sicher said, you should probably worry more about draw calls and optimising your gui scenes using layers than the number of gui scenes you have in your game.
Personally I don’t think it’s a bad idea to have for instance several different kinds of popups in a single gui, and disable the root nodes of the ones you are not currently using. You could also decide to put each gui scene in a separate collection, similar to what is done in this recently announced community library, but then you should also keep in mind that when you load a collection proxy you get a new physics world with all that it entails in terms of memory usage.