So if Alice dropped multiple kids way before the mc became her fuckbuddy, so why Wendy who's her great-great-granddaughter is the only 1 left & what happened to the rest of them?
I believe if I remember right it's implied that a majority of the rest of the village is actually her descendants as bunny girls, they just don't get counted as characters because they're in the background and none of them are as powerful as Alice or Wendy, plus they may not have as long a lifespan as Wendy or Alice herself, since Alice is the original bunnygirl, and it's implied that stronger people generally live longer life spans.
I don't recall anything implying Wendy was the last one, just that she was the closest to Alice.
Although they definitely don't have the largest population, given that by the MC's own account, at most there was only ever 3-4 males at peak in his village at one time, counting himself, his father who is dead before the story starts, and maybe 1-2 others from a separate family that moved out the village when he was younger, again, before the story even starts, and keeping in mind that the only bunny girl population in the world is Mistral Village, they simply wouldn't be able to sustain a large population before the MC starts his quest.
Keep in mind that at the start of the game, the village is mostly just Alice, her descendants, a few elves, the female cast, and ONE GUY who only just reached legal age, literally the day before the story starts. And outsiders weren't allowed in to protect those that remained, so there hasn't been any opportunity for anyone new to be born in at least a few decades, since the protagonist is 18 at the time the game starts, and his dad died with no other children because he wanted to stay faithful to his wife like an absolute chad, and there was literally no one else in the village of legal age until the game starts.
The stated reason for the village's population basically boils down to: No one can fuck enough to make babies. MC go fetch girls to make babies with so that the village doesn't go extinct by the end of the current generation.