I think its less of a friendship issue and more of the ability to "get" each other.

My co-founder and I have been working for almost 1.5 years on our startup. We have gone through so many iterations, we can see into each others minds. When an issue comes up, I know exactly what he is thinking and vis-versa. This ability is invaluable during negotiations, meetings, etc.

I don't think of us being on a friendship level, but its something greater. Its been said, its almost like your married to your co-founder - an analogy which is pretty much true. Your futures are tied together.