In Deathly Hallows, Aberforth mentions all the passages into Hogwarts were blocked. This means that Snape and/or someone else found out about the secret passage into Honeydukes:
“There’s only one way in now,” said Aberforth. “You must know they’ve got all the old secret passageways covered at both ends, Dementors all around the boundary walls, regular patrols inside the school from what my sources tell me. The place has never been so heavily guarded.”
— Deathly Hallows, chapter 28 (The Missing Mirror)
I don't recall Snape ever finding out for certain that there was such a passage, although the scene from PoA is probably evidence enough; i.e., when he caught Harry returning from throwing the mud at Malfoy.
HP Wiki has this to say: http://harrypotter.wikia.com/wiki/Secret_passages_at_Hogwarts
Is there anything in canon to suggest that Snape/Carrows actually knew about this passageway or is it purely speculation on Snape's part?