There are fanfiction communities that have strict rules about appropriate content. So, while the idea of Shinji and Rei pregnant might seem a bit out of the ordinary, it's possible to find stories where it's more about the development of their relationship in a non - sexualized pregnancy - like context. Maybe it could be about them taking on a new role together, like 'parenting' in a sense, an emotional journey of growth and discovery.
Yes, there might be some fanfictions that handle this concept in a more family - friendly or symbolic way. For example, some could explore the idea of a new beginning or a deep emotional connection between them represented metaphorically as a 'pregnancy' of sorts, without delving into inappropriate content.