I've found lower stances to be better for training, even if I don't use them as much in sparring. They're useful for training leg strength and dexterity. I've tried a few styles of forms in Taekwondo, some which utilize lower, deeper stances and others which utilize walking stances, and I've found I sweat a lot more when doing the forms with deeper stances.
My master has a background in special forces, and he's selected the forms with deeper stances. We use deeper stances in most of our self defense drills (sometimes using a shallower stance depending on the distance we need to cover. The practical benefits of deeper stances, I've found, is:
- More powerful base than a shallow stance (but shallow stances are quicker)
- Easier to close short distances with a large step into a deep stance than with small steps
- In a deep stance you have the option to change levels up or down. In a shallow stance you can only go down.
Of course, if I'm misunderstanding and you're talking about stances in which your rump is only inches off the ground, then maybe I could see your point (although they would probably help with leg strength and conditioning). Or if you also work out and don't skip leg day, then maybe you want to opt for the shallower stances because you don't need the conditioning of the deep stances. But these are the benefits I see.