It depends on the fan base. Some parts of the Naruto fan community might be really into this kind of fanfiction. They enjoy seeing different character interactions and exploring what - if scenarios. However, others might not be as interested as they prefer to stick to more canon - based pairings or storylines. So, while it has its own niche, it's not something that's universally adored within the entire fan community.
Yes, it can be a somewhat popular theme. In the world of fanfiction, pairing unexpected characters often creates interesting and unique storylines. Neji and Sakura coming together in a story where she is pregnant can explore different aspects of their relationship, such as how they deal with the upcoming changes, their friends' reactions, and how it might affect their roles in the ninja world. It allows fans to delve into a more domestic and emotional side of these characters that we don't often see in the original series.
I think it has a decent following. There are fans who like to see the development of relationships that are not explored in the original story. A Neji and Sakura pregnant fanfiction can bring in new elements like how the two characters from different clans would handle family planning, or how their respective skills would be used to protect their future family. It gives a chance for creativity to flow and for fans to imagine a whole new side of the Naruto universe.