I mean.... My comic is called Doctor Whoof, Legend of the Lunar Shadow. I've always opted for the less popular "whoof" because it sets my Doctor apart. It really is a matter of preference. In my headcanon Doctor Whooves is a ponyfied 12th regeneration of Matt Smith, while my Doctor, "Whoof" has always been a Pony. It's just how I choose to organize things.
Sort of? I don't know. The comic is fairly popular. For many people my doctor is their Fanon. No-body has ownership of the fan-created back-story of a background pony. Point is, I've heard both Whoof and Whooves used. simple as that.