I had to re-read parts of the story to get my grips on it.
For the first part, a while there I was thinking the guy was Neville, the whole plant thing was what threw me and the mention of "Professor" even though it's implied that Snape's not teaching anymore.
There were parts of this story on Harry's parts, towards the end, that I had to re-read. Yet, I still come away with the same feeling. Harry knew or at least suspected that something else was going on.
From what I gathered, it was just sex and convenience on Snape's end. Something he came into the habit of when he was still a Professor (perhaps why the shopkeeper still addresses him as such?) Yet with Harry, there is a real since of commitment and cherish and love.
It's like how some people can have affairs but still remain married to the one they love and that will never change.
Snape seeing Harry there with his back to him, sent a wave of fear through his body. He feared more the loss of Harry, the one he loves, than his 'lover' the man he is sleeping with (if it can even be called that, seems more like random quickies when convenient).
Yet on Harry's part. I sense a feeling that Harry knows that Snape is doing something. He may not know that he's being cheated on, but he's sending a message to Snape that he knows something is going on.
Harry rubbed his hand over the softness of Severus' sleeve, pressing his palm over the indelible skull and serpent. "You had everyone fooled," he said. "Especially me." His grin cleared with recollection, leaving his face blank.
"Give me some credit," Severus quipped dryly. "I wore that mask well."
Harry's eyes flickered; a moment later he blinked. "Funny," he smiled.
In the light of the mirror their gazes realigned, and Severus felt himself widen, further than before, his heart thinning at the edge into an inexplicable membrane of space and inconsequence, momentary but for the warmth of the hand now fitting to his.
Brilliant story. I like an infidelity every one in a while, but it depends on how it is written. This one I like.