I have done the Good NTR/Bad NTR/No Stilyo endings, but I didn’t bother hiding the father. I didn’t think there would be much change, but I’ll try that out as well now that you mention it.
I’ve generally enjoyed the game a lot. My expectations very much depend on the genre/style etc of the story. The world is very much not serious, which is why I’m not as bothered by the silly characters, designs, etc as some others seem to be.
The only single thing I consistently didn’t like was the penis model used for the girls. It is too ugly, but even that can be ignored for the most part.
Regarding the thousands of children: The calculation really depends on how literally you are supposed interprete the story. If you take it as a concentrated representation of her life, the "actual" frequency might be significantly lower. (Basically, the more interesting parts are put closer together to make it more narratively compelling. Therefore, more immediate sex, less down-time than the "actual" events.)
This is how novels "based on real events"/biographies etc are sometimes done, if they care about accuracy in the first place. It’s not exactly lies, but the events are arranged together and compressed to make it more interesting.
4000+ pregnancies is the very rough estimation if you take it as-written, and every week is like what we are shown. Given that it’s a non-serious universe, this is the interpretation I went with.