I read the The Hound of the Baskervilles a long time ago, but I don't think it would have been a good choice to have Sherlock gone in the episode. In the novel, it's one thing because it's a subjective narrative and when Holmes is not around Watson, he cannot know what he's doing. However, in the episode, the narrative is not subjective. We do see Sherlock and John apart from each other a lot in that episode, but they had to show us what both were doing. Otherwise, it would have just been sort of weird.