Hell yeah I remember this game. I still play it every year or 2 on my PC. The new Zelda (coming out end of this year) is supposed to be a lot like it. Maybe even better... Unlike the craptastic WindWaker...

Don't worry about the nerd issue, jac. I was a video game fiend when I was growing up, and so were a few of my friends, but we don't know calculus, and we never got beat up in school. Like west coast style said: the nerd part is up to him. Video games won't make him that way. That train of thought is as asinine as the moronic parents who blame music and television for the bad things kids do...
Just let him have his fun. Like you said, he's only 4. And as of right now, it's not hurting anything at all. Besides, video games will help him develop good hand-eye coordination. Seriously.