We have eight legged spiders, six legged insects, etc... It's just on our planet that the ratio of 4-legged animals to multiple-legged animals is pretty high. Maybe that whole evolutionary branch of 4-legged animals on Pandora just got eaten up by all those 6-legged freak creatures. And the Na'vi survived because, well, they learned how to throw spears.
Or they have leftovers of the other two legs in their pants. And they get cut off in a weird cruel irrational religious ceremony just after birth.