It depends.
1. Is it relevant to the genre?
2. Is it fun?
3. Can it be represented in the system at the level of detail provided?
It's pretty obvious to me why D&D 3e had no sex-based differences for characters.
1. It wasn't relevant, as the published settings were largely egalitarian to one degree or another.
2. It was designed to be a game with wide appeal, so why restrict options? Even if female Str 18 barbarians are in theory more rare, should there be a price paid for being that rarity, or should you get the same shakes as any other Str 18 barbarian?
3. D&D 3e doesn't have enough detail to accurately reflect real-world differences very well, much less modern genre fantasy where Red Sonja is a She-Devil with a Sword. Relative to each other, in D&D terms, males would probably rate +1 Strength, with an additional +2 for lifting purposes only, +1 to the Intimidate skill, and get +1 to hit and damage with thrown weapons, while females would probably rate +1 Constitution, +1 to the Sense Motive skill, and +1 on Tumble checks. At most. You can't justify even a two point spread on any Ability Score, or a +2 on a skill. GURPS does only slightly better.
In the real world, men and women are very similar in abilities. They have virtually the same intelligence, and except in very specific cognitive tasks that do not resemble most real-world tasks, virtually interchangeable specific cognitive skills. Compared to most animals, males and females are similarly sized, although men do have considerably more muscle in their arms. Women are a little more flexible. Men tend to be less empathic, women more, although that is highly context dependent; men also tend to be higher status and women lower, which also affects empathy.
There are basically two areas where men excel beyond what even the most accomplished women can do. First, there are astoundingly more male mathematicians, virtually all of whom do their best work in their 20s, rarely even into their 30s, suggesting that hightly theoretical math involves some of those very specific cognitive tasks I was mentioning. Second, men can throw things. Due to a combination of wider shoulders, more powerful arms, a different center of balance, and perhaps some motor neuron differences (which may be learned difference), even a fairly typical man can throw a baseball better than all but the very best women. Even things like weight-lifting do not evince a huge divide; while men are unquestionably stronger to a very significant degree, the actual amount of difference is not huge. Strong women are often stronger than only slightly strong men. On the other side, if you want to survive long periods of physical stress, perhaps involving huge caloric losses, you want a woman. Women also retain a lot of flexibility in their bodies, which men lose rapidly even as they get into their teens.
Things like math v. science, thinking v. feeling, multi-tasking, etc..... whatever you heard, in actuality, women and men are more alike than different. Men and women who are good at, say, aeronautics perform more similarly to each other than do a male aeronauticist and a male truck driver, at tasks of mathematics, spatial geometry. etc.
Now, in fiction, differences may be exaggerated... or erased (classically, the "tender" woman who cannot survive hardship, despite having birthed untold generations of humans in the wilderness). If you want to simulate THAT, look closely at the actual game differences you want to make.
