I think there are actual mythological foundations for all the Kami genders. It's just that the first ones were males. Here's my reasoning:
Apocalypse: In European tradition, the 4 Horsemen of the Apocalypse have been represented as male for centuries, and the theme here is clear, So it makes sense for our "4 Horses", if you will, to be male
Gate to the Dreamlands: These are inspired from Lovecraft (by the way, I am really impressed by this). I expect, although I haven't researched it thoroughly, that their genders are faithful to their characters of inspiration.
Cure the Love: I think that Amor is probably based on Cupid. Once again, his mythological predecessor is male, so it makes sense for him to be male.
Hoppers: No idea on this front. Maybe hoppers are protandrous sequential hermaphrodites (translation: they start life as a male and then switch to female at a certain age/ size/ environment). Maybe only males hatch from eggs, and females are born in some different way, like staying in the mother's pouch?
Carpo: Her mythological basis is an ancient Greek goddess. Based on a quick browse through Wikipedia, I expect the other 2 members of the seasonal triad to be female as well. I'm looking forward to the reveal of the designs.
Drakes: As artificial life forms, I'm not sure why they are gendered, except that their in-world story is that they are created by merging the energy of Kami from the portal with Dragons and Cockatrices. Since most of the Kami that have come through the Warlock's portal have been male, I guess it makes sense for the drakes to be male.
As several people have noted, the genders have little effect on gameplay, so I think the imbalance will be rectified slowly over time as more female mythology backgrounds are incorporated.
tl;dr : They have specific genders because reasons, not because no one was paying attention.
I often have some good pets in my Pound/Giveaways tab. Feel free to ask for one of them.