Theres some but I cant remember all of them. This is one http://www.mangago.zone/read-manga/oyasuminasai_no_ato_wa/
Tadaima, Okaeri
Tadaima, Okaeri -Kagayaku hi-
Kashikomarishita Destiny
So far there's tadaima, okaeri and Kashikomarimashita and the one mentioned above and that manga that has the word "hebi" in it about twins, one is alpha and one is omega and the omega was raped by the alpha twins friend, like that. There is also a SnK oneshot of leviXerwin having a baby. I have a list of implied pregnancy/omegaverse you can check it out if you like, i just throw mangas there if i think they fit in, and for rereading purpose
Romantic Joutou by Moriyo.
Yes
https://myreadingmanga.info/madobuchiya-nishin-chikuhyou-no-hanayome-orc-bride-eng/ My sincerest apologies I have disturbed you.(๑•ㅂ•)و✧
A Random thought just popped in my head but i'm actually curious to know. Are there actually any omegaverse manga where the omega is pregnant and/or actually has a baby??