Falling in love, for Simon, doesn't happen like it does in the movies, or in books. He doesn't just wake up one day and have this grand realization that he's in love with Raphael; not like he did with Clary, anyway. There is a realization, of course, but it doesn't come as some huge shock to him. After all they've been through, the battles, bringing one another back from the brink of true death, all the lingering stares, personal conversations in the early hours of the morning. It all just... makes sense to him.
It clicks, it is what it is.
There's a brief moment of 'oh no, not again', because he's been through this whole unrequited thing before and it's not fun, but then he goes about his day as normal. It's okay though. He'll be okay, because Simon is The King of Suppressed Feelings and Raphael doesn't need to know.