I haven't read too many issues of Superboy, but yes, my impression was that magic came into it fairly often. I vaguely recal an issue I read a good number of years back that featured quite a bit of magic, and Superboy was all but saying, "Oh, great. Not another magically transformed classmate!"
I can also tell you that (in the comics) it's not entirely uncommon for Superman (the adult) to come up against magic. In fact, if you polled a bunch of fanboys about Superman's greatest vulnerability other than Kryptonite, you'd probably get as many who said "magic" as "Lois Lane."
I remember I came across an official DC "choose your own adventure" type webcomic a couple years back in which Superman was facing off against the recurring magical villainess Silver Banshee. One of the things that came up if you chose the wrong path early on was Superman being struck down by the Banshee. "Always was... vulnerable to... magic. <thud>" (Well, the "thud" wasn't in the dialogue box, but the rest is word for word.)
Beyond that, magic showed up a couple of times in the series. Illusions of Granduer, Chi of Steel, Never On Sunday, Ghosts, and I've Got You Under My Skin all involved magic, as well as a couple of other episodes. Remember, though, that there's a reason those episodes are not exactly the most popular ones around. Soul Mates had magic, too, by the way, but it was a minor part of the episode (crucial to the plot, but not given much actual screentime) and it was in a more magic-friendly context.
So, FoLCs may not like (or may choose to ignore) the more comics-like aspects of the show, but magic is definitely in canon.
Paul
