Dr. Vegapunk's original bod was finally shown in One Piece Chapter 1066, "The Will of Ohara." Not only that, but it was revealed what he looked like 22 years in the past as well as in the current story. There happens to be a large discrepancy between these two appearances, and it ahs nothing to do with his age.
In the past, Vegapunk had a massive cranium, presumably to house his gigantic brain. In the present, however, the top of his head has been cut down to size. This raises the question of what happened to his brain.
What Could Have Happened to Vegapunk's Head?
In the past, Vegapunk had a head that was so large that it dwarfed even the eight-and-a-half-foot-tall Monkey D. Dragon; the rest of the scientist barely came up to the chest of the freedom fighter. If his brain was really that big, then it makes sense that he would be the smartest man in the series. However, it would also mean that there should be few other places that can properly store it.
Regardless, the present Vegapunk seems to have removed most of his brain if not all of it. He has what looks like the top half of an apple on a rod where the upper portion of his head used to be. Present Vegapunk also comes off as a little more dopey or absentminded compared to his past self, which could be another hint to the fate of his brain.
Vegapunk might have divided his brain among his six Satellites. This would line up with his Albert Einstein motif; Einstein had his brain preserved, cut up, and analyzed following his death. Vegapunk might have found a way to cut up his huge brain and place a piece of it into each of the Satellites while maintaining functionality for each piece. He might have also kept a reasonable portion of it in his main Stella body. The fact that the Satellites have different thoughts and feelings seems to feed into this idea.
Alternatively, Vegapunk could be keeping his whole brain in a jar, a common trope in science fiction series. Since the whole Egghead Arc is more of a sci-fi story than the rest of One Piece's fantasy, this would be an ideal way to stay on the theme. His brain could be atttached to a supercomputer, which is in turn keeping the Satellites and the Stella all connected.
Are There Any Hints to What Happened?
As for the apple top on the Stella's head, this could be what he's using to keep himself connected to everything else. It could be some sort of antenna or receptor that sends signals to and from the missing section of his head, wherever it is. If the Satellites really do have parts of his brain in them, then the apple could be connecting him to them, too.
Whatever happened to the rest of Vegapunk's head, it's clearly not with him there. The only apparent hints to its location are the apple top and the way each of the Vegapunks act, but there are still a lot of unknowns. In any case, it seems as though the original Vegapunk doesn't have the same mental capabilities as he once did, at least not all to himslef. One could say that he's not all there.