You never see female ones......
The Fallout 3 super mutants are all asixual beings, while in the other Fallouts they aren't (since I could take Marcus to a brothel, and he worried about the girl getting pregnant even though that was a joke since all super mutants are sterile... but in Fallout 3 they're not only sterile, they're asixual and apparently has no reproducive organs! That's why they constantly need other people to transform.)
Spoiler Warning Here! Read with caution.
What SavageBeating has said about the DC Mutants is 100% right. The FEV In vault 87 is out of FEV so no more DC super mutants. They still kidnap because they are dumb and that's all they know.
The West Coast Mutants are male and female. We don't see any female ones in fallout one or two but the graphics are alot different so maybe we do but it was not important to show. The first super Mutants were created by the master with FEV Vats at mariposa get taken out. (well the first were created before the war in an attempt to make super men but they were destroyed)
More Super Mutants were created in fallout two when the Enclave found Mariposa and started digging it up to get a FEV sample. The workers after spending so much time in the place became super mutant and the Enclave closed the place up. We can open it again in fallout two. Does this mean more people can find it and become super mutant? I don't know.
Fallout tactics Female Mutants are shown. There is even Super Mutant prosttute along with some ghoul ones.
There was a Super Mutant Scientist (yes a smart super mutant because west coast SM can remain as smart as they were when human) working on a cure for sterilization in super mutants. you have a couple options when at this Lab. You can A) take out the lab and kill everything. B ) Just do your orders and take out the power generators.
Doing good and just taking out the generators and moving on will result in the Midwestern BoS taking the Lab and the scientists back to an unknown bunker to continue the search for a cure. They do not destroy it because it's so important to the super mutants that they become whiling to help the BoS inorder to keep their project safe. A bargaining chip if you will.
So there are some questions left. The mariposa base is still open so others could find it maybe a new master?
Does the Midwestern BoS find a cure so super mutants (West Coast) can have kids.
If we don't get an answer to those and no more super mutants come from Meriposa or the Midwestern BoS does not find a cure (Or if we ever learn of anything at all from them) then that means all super mutants are Endangered.
DC ones will become older and bigger and more crazy. West Coast will just get older and die off over time. The ones in New Vegas must be getting to the point were they will start dying off. Marcus in fallout two as well as the others were already pretty old and that takes place 70 years before New Vegas.
So maybe more Mariposa Mutants or a cure was found or Other?