My theories as to why Raku is crying:

He knows he is going to have to hurt Onodera, but he doesn't want to There's a feeling of regret for not confessing when he "liked" her more then Chitoge/when barely even knew who Chitoge was The simple fact that a now long lasting relationship of hidden love for each other is about to end I don't really know about this one, but maybe he's crying at the fact he had all this time to confess but now it's useless (probably not lol)

I will give it to Onodera, at least she knew herself that Raku's love now was Chitoge, and came to terms by herself. She even told Raku her true feelings knowing that he didn't feel the same anymore. I'm sure that Chitoge probably hears the conversation as she's "just up the hill" and once again she will probably take it the wrong way before Raku or Kosaki will have a chance to tell her what happened, resulting in a confrontation with Kosaki & Chitoge. I'm really on the edge of my chair about one manga my god.