Yes even irl when a baby is born theyre immediately handed over to the mother/birthing person as familiarisation through immediate physical contact is needed for the baby to bond to their parents. yi-ho didnt get to do that with yi-rim so he didn't forge that bond with him, causing him to not recognise yi-rim as his dad and reject him.
Baby is so sensitive towards any feeling esp negative ones. They can sense it just like that and cry. For example, when someone got angry near them, they will stay quiet out of fear, and when someone's really sad they will cry as well.
I happen to witness my own baby nephew who was brought along to my relative's house and they just lost their son, so the situation was really sad. My nephew immediately cried without stop inside the house but also immediately stopped when their parents took them out from there.
I think in Yi-ho's case, he sensed Yi-rim's negative feelings towards him + he didn't recognize Yi-rim as his own daddy, the unfamiliar and negativity that he sensed probably what made him cry.
Yi-ho can sense pheromones even when hes only a baby, he can sense Cheong-ho that hes anxious, worried and sad (about Yirim leaving), he cant understand Yirim bec Yirim doesnt release pheromones so hes also confused. And doesn't like that Yirim causes his daddy cheong-ho anxious and worried like that. So when they alr talked it out, he felt cheongho finally got through his anxiety thats why he fully accepted his daddy yirim.
Those who has a degree of Bachelor of Science in Omegaverse can someone explain why Yi-ho was crying every time Yi-rim tries to touch him? (The early chapters of the side story) or it's just a birth thing?