Major major

So where did they go?

They are all there it's just that they sometimes don't show all three of them.

https://static.ichijinsha.co.jp/online/books/zerosum/castehate/castehate_E6UrYT10009/index.html

Plus they tend to playing around in the rabbit hybris monster's stomach.

Hamster mouth pocket? He put them in his mouth but didn't chew or swallow and then popped them back out.

Starting to feel like all 3 of them will be together. Maybe Snake needs both seeds for healthy long-lived babies?

Kyogokuin (rabbit) was probably just teasing Tsuki (anaconda) by hiding his babies from him. I think so as well, it feels like a three-way! If he was impregnated by another alpha the babies would probably live normal life spans. But honestly Tsukuyomi just probably has a love for beta dick. (=・ω・=)

Are all his kids (living and passed on) from Betas?

I think he was teasing the wolf more so than Tsuki, he is still upset at him for being close to Tsuki...but it might be lessening? Rabbit seems interested in Tsuki from what I can tell from the Raws.

Yep it's mentioned by Rurikawa early in the manga that Tsuki knowingly often has babies with betas even though they have short life spans.

Yep! It's mentioned by Rurikawa early in the manga that Tsuki knowingly often has babies with betas even though they have short life spans.