Here's a question, how large are the five villain factions supposed to be in direct members, not counting pawns, puppets etc.?
The reason I'm asking this is that from the first go, I got the impression that the Eaters of the Lotus for example were supposed to be perhaps a 200-300 sorcerous enuchs, primary appearing as featured foes or bosses, and then tons of non-enuch goons, supernatural creature slaves etc. but then I saw that one of the standard mooks in the book have such enuchs as, well, mooks to be blasted down by the dozen. Meaning to my mind that these enuchs would have to be many more than a few hundred individuals since they haven't run out of members in the Chi War or been overtly passive to my knowledge and they should also have an easy flow of new recruits ion their home juncture. Same with New Simian Army who are apparently to few to impose their will on the future and can't get new members, and the Ascendency who also can't get new members to my understanding and so on.
The numbers I myself am thinking about are roughly;
Personally, I have a hard time imagining a scenario where it would add any value to try to lock down these numbers in any exact way, any more than it would make sense in a James Bond movie to try to figure out exactly how many members belong to SMERSH or SPECTRE.
If those numbers add something cool to your game, that's awesome! I'd keep it vague myself, and not worry about it too much.
To me the value comes from knowing how to present the bad guys. If a factions is supposed to have tons of members, it makes sense to encounter them at virtually every turn and also as mooks. But if a faction is supposed to have few and more like elite members, then non-member goons and fewer but harder actual members presents that kind of sense to the players. But you are totally right in that exact numbers is probably unncessary even if I would say that having an idea if a faction is essentially an elite group or a mass movement is of some importance.
If a tranimal has kids with a similar tranimal, the kids inherit their special abilities. Most of the ascended are descendants of the original tranimals, they aren't the original animals themselves. Given there's been no magic in their timeline for several hundred years and they control the world with all the perks that entails, they could be quite big; hundreds of thousands in the modern era, if not more.
The problem I see however is that unless there were lots and lots and lots of tranimals at the start, they wouldn't have been able to produce these numbers due to inbreeding across the centuries and so shouldn't be all that many hundreds of thousands of tranimals today. But I do see your point in many human descendents of the tranimals.
Think "action movie logic". Does it make any sense in Hard-Boiled that Johnny can store his weapons under a hospital? Does it make any sense to send messages via weird musical codes? Not a bit! But it's awesome.
I wouldn't worry about actual rates of reproduction or how many transformed animals can pass on their nature to their children over time. Don't forget, there's also time travel through portals, and sorcerous magic, and the like!
I'd decide for each faction what the effect is, of how many people they've got. You don't need to know that there are only 1,200 transformed animals in the world, but if you want the Ascended to be worried about running out of members, you can just say they're worried about running out of members!