Quite frankly, it's usually because 99% of people who own Grade stallions are so irresponsible and idiotic, you KNOW the horse is worthless.
When it boils down to it, only an utter fool keeps a Grade stallion intact - a responsible breeder would never think of it. Mares are a bit of a different story - they fall into the gelding category, and you really can wind up with some decent looking Grade mares that fell through the cracks because there are so many of them. They have their entire lives to prove themselves, whereas there are probably quite a few geldings that WOULD have made good stallions, but were snipped by responsible owners who knew an unregistered stud doesn't amount to much.
Naturally this CAN happen with stallions as well, but MOST people have them gelded early enough that it never becomes an issue. Just stop for a moment and think what mindset it takes to go "I have an unregisterable Draft/QH foal...he'll make a good stud!"
As was mentioned, most of the REGISTERED stallions need to be clipped. We have more then enough to suit our needs, we really don't need to be keeping the mediocre or even "good" ones around anymore.