"In pace requiescat!" could be interpreted in two ways. The traditional Latin blessing could be taken as sarcastic and ironic, or it could be interpreted as being totally sincere. Since Montresor is now fifty years older and ready to die himself, and since he has rid himself of the hatred that caused him to kill Fortunato fifty years ago, it seems more likely that he means In pace requiescat! sincerely.
The purpose of revenge is to achieve closure. That is, to get rid of all the bad feelings and painful memories that inspired the idea of revenge. Montresor can no longer feel strong hatred for Fortunato after all these years. If he thinks of him at all he must think of him as a skeleton dressed in a few stained rags of his once gaudy jester's costume. Montresor has buried Fortunato among the remains of his own ancestors and must feel that Fortunato has become, in a sense, a part of the family.
Furthermore, Montresor is the only person in the whole wide world who knows what became of Fortunato. This must have been a topic of conversation for many years--and Montresor would have felt obliged to be one of the people to show the greatest interest for the longest period of time. This is because Montresor obviously took pains to make everybody, including Fortunato himself, believe that the two men were the best of friends. Montresor wanted to be above suspicion when Fortunato disappeared. He even conditioned himself to think of Fortunato as his friend while he was planning to murder him. Note that he refers to Fortunato constantly throughout the narrative as "my friend," "my good friend," and "my poor friend." He undoubtedly took every occasion to refer to Fortunato as his good friend when he was talking about him with others.
We can imagine the wonder and consternation that must have grown and spread after it was discovered that one of the city's leading citizens had simply disappeared right off the streets. There would have been official investigations and private investigations. Montresor would have continued to ask questions about his "good friend" longer than almost anybody else. Montresor had committed the perfect crime. He must feel not only satisfied but pleased. When he says, "In pace requiescat!" at the end of his letter, it is as if he is finally putting the subject out of his mind forever. He has been so successful that no one will find the body for hundreds of years. And if at some date in the distant future workmen might discover a skeleton in chains behind a stone wall, there would be nobody left to remember Fortunato or the mystery surrounding his strange disappearance.
The words In pace requiescat are normally said by a priest at a funeral. Since Montresor is the only person who knows when and where his good friend Fortunato died, he may feel it is incumbent upon him to pronounce those final ceremonial words himself.