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Of course Obama wasn't responsible, but it wouldn't hurt to apologize anyway as a diplomatic gesture on behalf of the US.
Because it was such an ugly thing to do, dropping nuclear bombs on cities. Not military targets, but cities full of civilians. It could be called an act of pure and willful terrorism, and there can be no justification for that, not even in time of war

According to Wikileaks, Obama actually intended to apologize in 2009, but Japan suggested that he shouldn't (for political reasons) so it didn't come to pass.

Regarding a Japanese apology for their actions in WO2, they actually did in 1995. It was criticized by China because it wasn't a written apology. The fact that some Japanese government officials are still denying the Nanking Massacre probably doesn't help either.
But none of that is a valid reason for the US to not offer an official apology for the nuclear bombs.