The difference is the shy guy won't say those things where as a guy who is not interested will say the wrong thing, won't apologise and will make a bad joke out off it. He will also most likely so subtle things that hint to you that he is not interested. Like calling you bro, dude, man when it is just you and him. The shy guy will probably call you and your friends guys, or dudes. Those words in many parts are non gender specific when referring to a small group.
If it seems like he is only giving answers or responses to your messages and isn't trying to continue the conversation at all, then he probably isn't interested. If he is asking questions about you then he might be interested.
A true shy guy will most likely unintentionally make a fool of himself in conversation. And probably apologize profusely for everything, even unneccisary things. It may be noticable enough to even annoy you, depending the intensity of it i guess.