After Watson and Henry have discovered that the mysterious L.L. is just a woman that Sir Charles Baskerville was going to meet on the night of his death, Henry asks Watson, ". . . what do you make of this new light?" Watson replies, "It seems to have left the darkness blacker than before." Instead of revealing the identity of someone directly involved with the murder, it only serves to introduce new elements to the situation, making it more confusing.
When Sherlock is discussing how they have no actual evidence against Stapleton, he says, "If he were acting through a human agent we could get some evidence, but if we were to drag this great dog to the light of day it would not help us in putting a rope round the neck of its master." The titular hound is associated with the darkness of night, and Holmes and Watson know its description cannot entirely be based in fact, as it is too big and hellish to be a real dog; in this quote, Sherlock discusses pulling the hound away from the lies and shadows and revealing it for what it is in the clear light of day where it can be seen for what it is.
After the fog has begun rolling towards Holmes, Watson, and Lestrade while they wait for Henry and the hound to appear, there is this sentence: "The stars shone cold and bright, while a half-moon bathed the whole scene in a soft, uncertain light." The half-moon provides only part of the light that it could, and so it is not as bright as it could be, making it an "uncertain light"; the truth will not be completely visible to them, especially with the fog, which makes their perception of their surroundings "uncertain".
Finally, there is some description from Watson about searching for the convict by following the light of his candle: "There is nothing so deceptive as a light upon a pitch-dark night . . . But at last we could see whence it came, and then we knew that we were indeed very close." This quote is possibly referring to the idea of there being an element of truth amongst lies and how this makes such a case more difficult to solve until you get closer to the truth. In The Hound of the Baskervilles and also in the episode "The Reichenbach Fall", there is some deception going on which has elements of truth but is otherwise composed of lies, and this helps make the deceit believable but also harder to disprove. In The Hound of the Baskervilles, there is a hound killing people out on the moor, but it isn't supernatural, and it is enabled by a human owner as opposed to working alone or being controlled by a demon or the devil. In "The Reichenbach Fall", Moriarty's attempt to make Sherlock out to be a fraud involves truthful facts from Sherlock's life, provided by Mycroft Holmes, and outright lies.