I shipped it since the very beginning
I feel like there have been hints to Yuiji possibly falling for Yamato. The way he said "I want to help him" and how he kissed his check. I know that's obviously because Yuiji immensely cares for Yamato but could possibly be signs of him seeing him as more than a friend. Personally I feel the effort he puts into Yamato is a lot MORE than he has done for other people (no offense TO Yuiji) Its also HOW hes so comfortable with Yamato and how he even said "I feel so relaxed around you". I feel as if they could be hints.
Well sometimes the fact that you can still become friend with them is already enough for some person. As someone who i think is currently in love with my best friend from back in high school, sometimes i feel, just be able to talk to him and hang out in his house every time i go back to my hometown i already enough for him. I don't really ask that much and I already give enough by fact that he still accept me as his friend after he accidentally found out about my sexuality. I think Yamato is also that kind of type especially looking on how he treat Hongou. For other it can be unbearable but for some seeing them smile is already enough.
While I too would be content if this is just a story about friendship and dealing with who you are, I actually think there's evidence that affection can happen even if it would be one sided. While I have no idea if Yuji would ever lean to liking men, I do think as of recently Yamato has been seeing Yuji differently. This isn't just me being someone that wants gay for the sake of gay, but I think the author has made some deliberate choices in making Yuji "shine" in the eyes of Yamato. I could be completely off my rocker, but the scene where they are sitting on the bench and when they slept side by side looked as if Yamato was quite stricken by Yuji.
However, if the author continues writing closer to how the real world works, then I'm a little afraid if that would develop into a one sided love. I have had a couple of gay friends that couldn't help but fall in love with straight people, just because their pool to choose from is so small. It's truly heartbreaking to watch. Either way the author has done a fantastic job, and this is one of the few shounen ai's that I think deserves 100% recognition for it's depth and heart.