Dr. Fate was initially not magical at all, he was atomic! Nabu taught him ancient forgotten sciences including control over the power of the atoms. So, he was more of a cross between Captain Atom & Firestorm. Wotan was said to have the same knowledge. There are some stories where he actually discounts the existence of things like ghosts! I guess the writers were really going for the idea that a sufficiently advanced science would appear to be like magic to a primitive culture.
The thunderbolt was powerful but his powers were limited to having to being commanded and a time-limit. He did sometimes fudge the rules a bit in order to help Johnny. Whether he was actually magical opposed to due to his being from the 5th Dimension thus bound to different scientific rules and limitations is an interesting distinction I don't know if really explored.
I can't believe I didn't know that about Dr. Fate! I haven't read any of his Golden Age era, only Bronze and beyond. Sounds like the change they made with The Phantom Stranger. It's funny how when the book started it was like the X-Files; you had Dr. Thirteen explaining crimes that appeared supernatural as actually being explainable by scientific logic and then the Phantom Stranger shows up and tells him how it might actually have a supernatural cause. Stranger has no powers at all, he's simply terribly mysterious. Then all of a sudden a couple of years into his run they ditch that format and he's flying around, shooting energy bolts out of his hands, fighting witches and demons. He really became the gimmick, I guess.