Is there anyway to add new (user) sub categories to media by?
Normally, no, at least not in a proper way that I know of, but maybe other users know something more about it.
You may want to have a look at this thread which gives a solution to our need for customising groups.
Now, if you really need to add custom categories, subCategories to your presets, this can be done, outside of cubase by editing the mediaBay database. However, this will not let you choose the created categories, subCategories for a new preset afterwards, as you most probably would like, if I understand your aim correctly. It actually surprises me a bit, I just don’t know why mediaBay multiComboBoxes are not getting populated based on the db’s content and they’re using another path (?)
Anyway, here’s a screenshot with a preset and its custom category and subCategory made to demonstrate editing externally the database, which - in my opinion - should be avoided: