Quite a bit, actually. Yes, the original Ditko issues have a certain innocence about them, but at bottom existed a hardened cynicism about viewing life from the outside. It's been pointed out that comicdom's obsession with dual identities stems from the fact that a great many of the creators were Jewish. Certainly very few heros conformed to the "blonde, blue-eyed, all-American" ideal. Superman, Batman, and Spider-Man were all dark haired outsiders who were feared and despised for what they were, rather than what they did (which was always good). It wouldn't be a stretch to say that Lex Luthor or J. Jonah Jamison represented a typical anti-semite in their unreasoning hatred of Superman or Spider-Man. In that sense, the alter-ego (Clark Kent, Peter Parker) represents the Jewish American experience of assimilation. How many of these writers and artists overheard anti-semitic remarks by people who didn't know that they were in the presence of Jews? After all, Stanley Leiber changed his name to Stan Lee. It's not difficult to imagine that Peter listening to one of Jonah's anti-Spider-Man diatribes (unaware that he was in the presence of Spider-Man himself) refers to this experience.
that particular piece of substance is more in the mind of the reader than in the mind of the artist I'd say. Not to downsize the importance of the comic medium in dealing with "issues," but they issues largely seem to have been there as a reflection of the times, not necessarily as an artistic reworking of the same.
Of course there are archetypal (and modern archetypal) themes used everywhere in the comic medium, those are the stuffs good stories are based on. The golden age spidey stories were certainly pretty well told, but to go so far as to say they had a lot of big great deep substance is a bit of a stretch I think.