Hi! I have to say this is a fascinating take on the situation! :D I admit I considered the idea of Harry secretly knowing...although more often I decided that Harry really didn't know. It often happens to me this way--I debate what characters know and don't know, what their motivations are, as I write, and certain things I fix but certain things I can't, which is why I think a lot of stuff I write ends up a bit ambiguous. :D My explanation for Harry really not knowing is this: he went to the same potions shop because Severus tells him he goes there--he doesn't hide from Harry where he is, how long he stays--he would answer any question Harry put to him. So Harry would ask him, where'd you go? why do you like that shop in particular? And Snape would tell him, I go to this little shop that's kind of obscure, because they've got the best quality ingredients. And it's all quite true. And then, when Harry's face goes all blank and introspective, he's thinking back on the bad old days, that's all. He's thinking how horrible it was to see Snape getting bitten, to see Snape die...
BUT. Maybe he knows, all along. (In the end I chose not to go this route explicitly because I'd written a Harry/Draco fic using that approach, and I didn't want to do it again. :)