@avgjoegeek > Dense MC's always drive me nuts with missing the obvious signs.
I don't think Senpai is missing the obvious signs. I think it is a case where he doesn't believe the obvious signs.
Before Nagatora came along, he was a loner. He clearly suffers from low self-esteem and a lack of confidence. So from his perspective, he can think of no real reason that Nagatora would be interested in him, even as he recognizes what appear to be clear signs that she might be interested. As such, he likely believes that if he were to acknowledge some feelings for her, she'd laugh at him, then teaser/bully him some. In such a situation, the safe path is to never confess, pretend the signs aren't really there, and just move on.
In a weird sort of way, because Senpai doesn't fawn over Nagatora, despite clearly being aware of her as a hot young babe, it likely makes Nagatora want to hang around him more.