KushchokhaniAh yes, that's right. That definitely makes the "double subject" explanation nonsensical, since any time we say "of which," we will follow with another noun. That just isn't what's wrong with A.
I agree that which/them creates the problem. Specifically, "of which" already accomplishes the task of introducing a subset of the preceding noun. So when we say "of them," it's redundant and distracting. We can just say "of which some have a population less than 10,000." However, even that is not great. Why not just say "some of which"? While we're
allowed to put "of which" first, it is most useful when the noun portion is long or has multiple parts. For instance, I might say "The committee consists of 10 members, of which 2 are administrators and 3 are science professors." If I didn't put "of which" first, I'd have to say it twice: "2 of which are administrators and 3 of which are science professors." For something as simple as our original case, the inversion doesn't really serve a purpose. I'd use "some of which have" here, but the OA of "some of them having" serves the same purpose.