Evil... is a bit of an odd term.
I mean, essentially, what is evil? It's difficult to define, and the general conception of it as a trait, a characteristic, as though "evil" is a driving force behind our actions, isn't very substantial. I mean, no infamous historical figure-- and please, let's not start a war over this-- has ever committed a crime, even a war crime, with the intent of being evil. Maybe they wanted power, maybe they were simply a sadist, perhaps they weren't mentally stable, they may have had extreme, irrational views and fears, and in the end, they're a terrible person either way, but I'd argue that "evil," in and of itself, doesn't truly exist.
As such, you'd have to find what exactly makes the HMS "evil" before you can simply say that he is. In my opinion, what led him to be necessarily "evil" is far more relevant than whether he truly is or not. That said, I mean... yes, the HMS is a weird guy, and I assume that's what you meant by "evil"--having a maliciousness beyond what he intentionally displays. Still, even in that case, I'd argue no.
But don't get me wrong-- I certainly agree that the HMS has a terribly cruel side to him, though not in a way that makes him "evil." Firstly, I'd like to point out something central to his character-- masks; see, you could argue that the Happy Mask Salesman utilizes what is practically a mask of personality in displaying himself. We've all seen it: he's perfectly fine, well-mannered and well-spoken, when suddenly, he snaps; red eyes, a scowl, rage spilling from his tongue, so much so that he can't think straight, can't speak straight-- what he shows here is what I'd liken to his true character, and his well-mannered self, I believe, is his mask.
So, what does his mask represent? I mean, masks are meant to disguise who you truly are, so how is he trying to portray himself? What is he not, essentially, at his heart? What cavity is he trying to fill? Well, the words of his masked self give us some insight: He says he "Believes in Link's strengths"? Doe he? Or is he simply offering false security? What about "I'm a very busy fellow, and I must leave this town in just three days"? Obviously, we all know his urgency has nothing to do with his schedule. but rather with a much more grave issue, the moon's descent and subsequent obliteration of the world. What the HMS is trying to sell is his well-being; that, despite the chaos of the world around him, he is a stable, collected, moderate individual. Thus, following the logic of his two selves and their relationship, he must be the complete opposite: unstable and obsessive.
And... wow... That was a lot of work to get to a point I could've covered in my first sentence. But anyway, these three traits do an excellent job of summing up the HMS' character, especially his fascination with dark arts and artifacts, and, ultimately, that's really all there is to his character. My senses tell me he's simply an incredibly sickly man-- once again, not "evil", per se, but, due to his disturbing nature, capable of performing harmful and immoral deeds for his own gain and to bring his warped sense of rightfulness to fruition. He likely has a shadowy past, but not necessarily a supernatural one; his eery abilities are likely a result of his shockingly expansive wealth of knowledge, having evidently delved into the forbidden pasts of multiple tribes (the ancient tribe of MM and the Sheikah, to name a few), among other dark studies of his, all likely to to his, as noted, twisted and obsessive nature.
And, in the end, that's more fulfilling than any any empty theory of his relations to the ancient tribe, the moon children, the Twili, etc. In the end, at least to me, all of the fright, all of the fear, put into any otherworldly phenomena imaginable, any paranormal conspiracy conceivable, pales in comparison to the utter terror of a man who knows more than he should.