We are first introduced to Stapleton as a fairly innocent naturalist living on the moor with his sister, but there are some clues early on.  First of all, he seems to know the moor well.  He knows his way around, and can avoid the traps.  This does seem appropriate for a naturalist, but it also allows him to keep his hound in secret.

The second clue is Stapleton’s sister.  He is adamant against her developing any kind of relationship with Sir Henry.  This seems odd, because a marriage to someone of that wealth would normally be encouraged by a brother.  There is also a reference to his past as a schoolmaster, with the hint that things did not go well in the end for the school.  Stapleton also seems a little more than neighborly in his interest in the Baskerville household.

Stapleton encourages the rumors of the supernatural carefully.  When asked what he thinks, he does not really deny the existence of the hound.

Stapleton was guarded in his replies, but it was easy to see that he said less than he might, and that he would not express his whole opinion out of consideration for the feelings of the baronet. He told us of similar cases, where families had suffered from some evil influence, and he left us with the impression that he shared the popular view upon the matter. (enotes pdf p. 55)

Holmes realizes that there is a real hound involved when the new boot is returned and an old one is stolen.  Only a hound would need an old boot for a scent.  He also does research on Stapleton and find out that he is using an alias and his sister is really his wife.