Summertime Saga, which admittedly should have been on that list, it is a little more cartoonish in art-style, but it is open world, pregnancy and birth and re-impregnation, and pretty funny from what i remember. The children 'disappear' from the game once grown up thou
theres also another game ill mention, but it has zero story, because it is not a visual novel in any way shape or form, it is in fact a medieval, survival, 1st-person, city builder - Medieval Dynasty - and it get a mention because it does indeed have pregnancy - you get to build a village, recruit girls to work in your village (well, you can recruit the guys too, but who does that??) you can actually marry one of the NPCs that inhabit your village, get them pregnant (no sex scenes) and the child then develops into an adult and when your character dies of old age or otherwise, you take over as the 'offspring' to continue the game, assuming they have survived, thus propagating your dynasty. no kids = game over.
(actually you should recruit guys also, cos they will reproduce and grow your village also)