I don't think so. You see, the HH has explained which Link's are the same. And also, SS explains that each Link is usually just a reincarnation of sorts of the original Link, or at least a descendant. The Oracles Links are the same, OoT Link and MM Link are the same, and I believe PH and ST have the same Link. Other than that I think all Link's are different.
EDIT: Okay I just reread your post and I see what you mean now- as in, because the events happen in different timelines, they could be the same Link going through a different course of events. Well, I'd have to say that's entirely possible in the case of WW and TP Link, but I would say those are the only games where that could be a theory. I mean, sure, they could be the same Link but they are born into completely different circumstances so they're not really the same... same background? The game wouldn't indicate that way canonically... god, this is getting philosophical.