Hi, I'm the guy behind Gygax magazine. It really made my day to see your comment. Thanks.
I think ads work in magazines like that because they're for audiences with specialized interests, and because a magazine ad isn't as intrusive, and hopefully doesn't get in the way of reading.
We do a PDF version of the magazine as well, but I'm trying to think about what else we can do to keep it relevant for people that don't read those formats.
And of course, both magazines featured wonderful cover art. "Dragon" had a huge variety of artists and featured some really unforgettable pieces and Byte often featured Robert Tinney who perfectly captured the zeitgeist of the computer revolution with his simple, clean, but imaginative artwork.