so I'm thinking there are probably more adult females around than chaco, and in a similar way to how video games "conveniently forego" showing absolutely every nook and cranny and inhabitant of a world because that would take too long, take too much effort and detract from the game itself, they just aren't show. for example Maridia "just plain didn't exist" in Metroid or even Metroid: Zero Mission despite the fact that we know it's there in Super Metroid and it didn't just sprout inside Zebes between the half-decade or whatever between Metroid and Super Metroid. Or how that ice mountain region of Hyrule didn't seem to exist whatsoever in OoT despite the fact it's there in TP, which is just a few hundred years after OoT/MM, alternate to WW. And a million other examples I can't think of. Basically, there may be more areas with more Mimigas hiding throughout the Island that we never see, or even more Mimigas in the village/plantation/grasstown that we just plain never see period.
I think the random prisoners/Shovel Brigade/caged Mimigas at the King's Table all kind of represent the "several random mimigas all around the island" or whatever, and aren't meant to be actually considered the complete set of individuals that might be in that situation or even considered necessarily "male" or "female" (and besides, the ones at the King's Table it could be considered are implied to be female). But yeah, it's like any number of old NES-era titles that Cave Story is paying homage to as a game, in which being able to count the exact number of sprites in a crowd at a sporting event may not mean that the developer intended there to only be like 50 people there but just couldn't be assed to show you absolutely every single person. I think if there were really, seriously a "shortage of women" problem for the Mimigas it'd have been mentioned somewhere in some form, as a sort of "we're a dyin' race, man" sort of thing, but it never was.
But then again, maybe it could be inferred that Santa is down on Earth in the ending to find some human (or rabbit?) booty with which to form some halfbreeds due to the lack of girls. And notice Chaco's with him. Maybe Chaco's there for the same reason, and is actually a man dressed in drag; they're plotting how they're going to go about it. Doing it with tons of humans and making a lot of creatures that look like Enraged Sue.
I'm... okay with this.