As of version 7.0, Ardour does not provide a way to reorganize clips in the main custom folder. For the time being, it is suggested to use a file manager to manage the folder.
As all the clips you already added to the project have been copied, you do not need to close Ardour to reorganize clips in the custom clips folder. Feel free to create new subfolders and move files around. All the changes will be reflected in the clips browser after you switch to another folder and back.
You do not need a fast drive for custom clips folders. Playing back a short clip will have little impact on the performance, and copying a file into the project should be likewise fast even from a hard disk. You can even use a network drive to store and access all your clips and loops.
There are three major ways to add new clips to your custom Clips folder.
Changes will take effect in Ardour once you switch to another folder and back.
Likewise, changes will take effect in Ardour once you switch to another folder and back.