It's pretty much cannon. But the relationship they have is not sexual at all. It's only platonic in this case. (Meaning that it's very intimate but never sexual)
Now they DID Kiss in both the novel and anime. Where I live that's considered 'gay', but to me it's more of a close friendship kind of kiss.
No.6 is a mild Shonen-ai. Not really gay but not exactly straight.
It is quite obvious in the manga and the anime that they are cannon, but in a tasteful manner. Their love is more than skin deep, and their relationship has been tested mutlitple times, only to be proven that it's for real. Although some peole like to claim they're "just close friends" or that they have a "brotherly" relationship, I find that hard to believe. I know many guys who have close friends, but never ever would they kiss them, especially on the lips, even to prove a point. Some peole just don't want to label No. 6 as a yaoi or shounen ai, becasue they are either against such things themselves, or they don't want to put a "taboo" label on it.
Here's an image from toi8, the people who did the offical art for the anime.
So yeah long story short, they're an item : )
Not really. It's only everyone's imagination. They do kiss and they do LOVE each other so they might be gay, but they never has sex, so I'm not sure.
The manga and anime are both rated YAOI, so yeah,...
Their relationship is definitely more than platonic, but it's not overly sexual either. They have strong feelings for one another and Shion actually changed Nezumi's way of life. Their love runs very deep <3