Absolutely, I think one's guilt is much worse if one's wrongdoing is never discovered. Clearly, the murder of Fortunato has been weighing on Montresor's conscience heavily because it has been around fifty years since he abandoned his nemesis inside the crypt's wall, and yet the memory is occupying his last moments on earth.
It appears, from the first and last lines of the story that Montresor is an old man, on his deathbed, and he's making his last confession. He supposes that the person to whom he speaks "know[s] the nature of [his] soul" well, and he says, at the end of the story, that for "half of a century no mortal has disturbed [Fortunato's bones]." Moreover, Montresor employs hyperbole (overstatement) in the story's first line in order to emphasize how wronged he had been by Fortunato, as if to justify the murder. He says, "The thousand injuries of Fortunato I had borne as I best could, but when he ventured upon insult I vowed revenge." It is improbable the Fortunato had actually harmed Montresor to any significant degree, but it certainly felt as though he had to Montresor. In offering this exaggeration, it appears that Montresor is attempting to reassure himself that his crime was justified (which is precisely what someone who has an unwanted guilty conscience might do).
Furthermore, in the final paragraph, Montresor says that after he'd begun to wall Fortunato in, "[his] heart grew sick; it was the dampness of the catacombs that made it so." It seems unlikely that the humidity in the crypt would cause his heart to pain him; it might cause him to become short of breath but why would it affect a part of the body so much associated with the soul, with morality and feeling? He seems to be offering, now, an excuse for why it felt so bad because he doesn't want to admit that it was guilt. If Fortunato truly deserved what he got, as Montresor seems to want to believe (and as he seems to want his auditor to believe as well), then there'd be no reason to feel guilt. And yet, it does seem a lot like guilt. Had his crime been discovered, it would have been out in the open, and he would have been punished for it. However, this way, having kept the secret for half a century, has clearly taken a toll on him: he is still so concerned with trying to justify his actions so that he does not have to come to grips with the weight of his own guilt. Yes, secret sin is far worse than public.