We know for sure that Roy and Hughes met while at the military academy since chapter 59. It doesn't seem likely at all that they knew each other before then. There're a couple of images that are most likely "photos" of that time they spent together, but we actually haven't "seen" anything of those years. It looks like in 1908, when National Alchemists were dispatched to the front, was the first time Hughes and Roy saw each other ever since the academy. They could see they had both changed.

Hughes: You... you've got a different look in your eyes.
Roy: You do too. It's a killer's eyes.
Hughes: Yeah. [...] It feels familiar, like it was just a while ago. Your eyes were sparkling at the military academy. We all sure talked a lot about this country's future.
Roy: Yeah, we sure did. About the "beautiful future".
Hughes: Aah, man. This stuff wasn't included in that future.

I consider Hughes to be a man as complex as Roy at least; he's not just the easy-going funny guy people perceive when they meet him. And it's also not as simple as "he's the opposite as Roy" or "they're the same in the inside" either. Some of Hughes' characteristics are similar to Roy indeed, they're both smart men with a peculiar sense of humor, quite weird and out of the ordinary. It's not hard to see why these two would get along very well.

They're both sensitive men, they've got no problem figuring out other people's feelings and dealing with their own. However, Roy is a far more idealist and naive man than Hughes. Actually, while you can see quite a few boyish traits in Roy's personality and lots of them in Hughes' actions, Roy's friend is a much more down-to-earth, practical and cynical man than him. There's some part of Hughes' personality that's even, dare I say it, selfish. Not towards the people he loves that are close to him, but he's got his priorities set and the greater good comes a lot lower in his escale than in Roy's.

     

Hughes: Haha...your way of thinking has changed, but your roots are still green! So... which means. If you're going to protect the entire country, you'd need to be at the very top of that progression.
Roy: It would certainly feel good up there, Hughes. But I can't climb up all the way with only my own power. I'm confident about that.
Hughes: What are you being so haughty for! Sounds interesting. I'll take a shot at it. I want to see how your green ideals would change the country that was built up by that King Bradley, who doesn't even fear God.

Of course, that's not a bad thing at all, it's a matter of personal choice and no one pushes you to care about other people more than they care about you. However, Hughes is still an idealist at heart, even if to a lesser extent than his friend, but it's precisely Roy the one who manages to bring that idealism out. Even if he's got a certain "hey, why not?" attitude towards the whole idea, he's the one who pushed Roy from below first. He gave him the first kick, the possibility that he could change things if he tried to. I think he got caught up in all that a lot more than he intended to in the first place.

They were both affected by the Ishval War, in one way or another. However, Roy was the one more wrecked by all of it. Hughes was after all, a more practical man, who knew exactly why he was fighting: to survive and go back home. Roy, being a little more fragile in spirit at that time, was tormented by his failure to use his power to protect, not only some people, but everyone. I think Roy and Hughes were very good complements for each other. Hughes learnt to believe that some naive ideals could be reached, while Roy adquired a more realistic point of view which he used to rebuild his dream.