You couldn't really "deny" that Pearl Harbor took place unless you wanted to ignore all news as fabrication. The attack on Pearl Harbor was part of a coordinated Japanese assault that include such targets the US-held Philippines and Guam, and the British-held Singapore and Hong Kong. The Japanese intended to preemptively cripple an American naval response to their invasions by attacking Pearl Harbor, and at the same time (the same day, at least) they did indeed launch those invasions. The Japanese government did not (could not) deny that this was its intention.

Yes, absolutely, in the sense that there were/are people who think Pearl Harbor was sort of an inside job. Not exactly in literal way that Truthers think--the predominant narrative, it seems, is that the government took empty planes to the WTC and blew it all up with preplaced bombs, and it was a missile at the Pentagon. So with Pearl Harbor, I don't think there's anyone of any significance who believes that Pearl Harbor was attacked by the US govt who then made it look like Japan. But there are people who think that the US knew that Pearl Harbor was going to be attacked on 12/7/41 and who deliberately did nothing to warn anybody or prevent it because they wanted it to happen in order to get public support to enter WWII. There are people who espouse this belief in both the US and Japan, by the way. But it is wrong for a variety of reasons.