Why aren't there any women super Grandmasters (GMs)? In chess you don't need to be physically strong. Well, you need some kind of endurance, but is it the real reason why there aren't any super strong women GMs?

Yes, I know about Hou Yifan and Judit Polgar, but they aren't even close to being world champion.

I understand that there are a lot more men chess players than women, but how many women are in top 100? Even the disproportionate number of players can't explain this.

What is the reason then? Can we deduce that men are smarter than women or shall we conclude that there are more geniuses among men than geniuses among women?
I don't know a lot about chess or even gender differences in cognition, but I do know enough that chess involves certain aspects of cognition and that there are gender differences in cognitive ability. For your question, about the number of super GMs, the average abilities of men and women is more or less irrelevant. You need to look at the tails of abilities. Again, there are differences in the tails. Men are better (both on average and at the extremes) for some abilities and worse at others. Women tend to excel at verbal and social cognition while men excel at spatial aspects of cognition.

In addition to cognitive differences, men and women react differently to competition and my guess is you cannot be a super GM without a strong competitive side. There are also social and cultural differences between men and women. Even if there were equal numbers of recreational players, that doesn't mean there would be equal numbers of competitive players (or similar rates of individuals willing to dedicate their lives to chess).

The popularity of competitive chess may well stem from its emphasis on male dominated traits (i.e., spatial cognition) and its lack of emphasis on verbal and social cognition.

The source of these gender differences (i.e., nature/nurture or intrinsic/learned) does not really matter, as the end result is that there are differences. As to whether these differences can explain the lack of women super GMs, it is not clear. That said, given there are measurable differences in cognitive abilities, reaction to competition, and social and cultural influences, it seems wrong to conclude that the lack of women super GMS means that men are smarter than women or that there are more male geniuses.