I love reading your thinking behind the motivations about Snape and the others involved :) I can completely understand how Snape could objectively look at the affair and see it as nothing special because of everything he was doing for Harry. Snape had to do a lot of justifying, and separate feelings from actions about the things he did as a spy, for Dumbledore and Voldemort that he'd have no qualms about justifying the reasons he had the affair with the shop-keeper. I can separate feelings from actions in the same way so it's very plausible for me about Snape's behavior. He and I just disagree on the rightness/wrongness of it for whatever his reasons ;)
It does show a flaw in Snape's thinking that he could save the relationship with Harry if Harry found out. I think it would be Harry's ability to forgive and to love that would save the relationship, not because of Snape's belief in his ability to have Harry forgive him. That sounds more like manipulation on the part of Snape, not in his belief that he did something wrong. I don't know about Harry, but I would find it difficult to forgive someone who thought they didn't do anything wrong in having an affair in the first place despite loving their partner. Snape has been able to save Harry through physical actions, that doesn't mean he could save a relationship through love. Because Harry's love for Snape is probably very deep, I think he'd be extremely hurt and wounded if he found out, and that's probably part of the reason Snape doesn't want Harry to find out, and why Snape noticed how he himself looked like when he was surprised by Harry in the shop. He didn't want to be caught, he knew what he was doing was wrong yet it still wasn't enough to stop him from going back again later.
Yeah, it would be very difficult for Harry to hide an attraction to someone else, he's so open and Severus still has his instincts as a spy of observation that he'd figure it out if Harry was having an affair. And Harry is more likely to give himself completely into an emotional affair, just like he does with his friendships.
Thanks for the explanation. I'm glad you took the time to explain your thoughts on the background to this fic :)