User blog comment:FairyRaven/Fairy Tail Chapter 366: 1000 Souls, Review and Commentary/@comment-6904925-20140110110507/@comment-7418318-20140110113120

It's possible that the smell of men and women is different enough to mask the similarity between father and daughter.

Or that Natsu's nose grew more sensitive over time and wasn't sensitive enough to pick up on the similarities when he joined the guild and by the time it became sensitive enough, he was so used to the smells of them that he never mentally made the connection.

Or maybe the smell of the alcohol that Cana is drowning herself in, is enough to overshadow any similarity to her and Gildarts' scents.