It doesn’t bother, because all the vstpresets you are creating will be saved, for a Windows based system, in the following path (I don’t know for an OSX based one) :
Creating a new folder will be visible only in Explorer/Finder at first : it can helps to organize vstpresets in an OS level, but will be usable only if you use the Media>Path attribute in the results view settings, either in Mediabay or when using the Load preset… command.
Actually, the first time we create a custom vstpreset for a given VSTi, a folder with the plug-in publisher name is created and inside it, also a subfolder one with the plug-in name, this time, and all the vstpresets that will be created after for this instrument will be put in it. If you use the New Folder button, you actually create a subfolder in the latter.
So, it is not recommanded trying to change the path of all the vstpresets, whether they are bundled with Cubase instruments or from you, as the aim is to be able to retrieve and back up all the vstpresets from one location (the path above). I don’t even know if it’s doable in a reliable way…