Akama, and literally every other Broken that can stealth, all quite clearly prove that yes, you can stealth with hooves. There was precedent for Draenei rogues literally before they were added as a playable race, and I think the Grimtotem rogues were added with Cata.
It isn't a hoof issue, and the fact that pandaren can be rogues just makes it worse. Male pandaren are quite fat, I don't believe they'd somehow be more stealthy than a Draenei or Tauren.