I'm not sure of specific titles off - hand, but you could start by looking on fanfiction.net. There are often a lot of stories in the Star Trek section that might include this theme. You can search for 'Kathryn Janeway pregnant' in the search bar and browse through the results.
One idea could be exploring how her pregnancy affects her leadership on the ship. Maybe she has to balance her duties while dealing with the physical and emotional changes of pregnancy. Another plot could involve the reactions of the crew. Some might be overjoyed and protective, while others could be worried about how it will impact their missions.
One common theme could be the challenges they face as a couple with a pregnancy in the context of their Star Trek adventures. Maybe dealing with the unknowns of having a child while being on a starship or in a strange part of the galaxy.
Finding good Chakotay and Janeway pregnant fanfiction can be a bit of a hunt. Another option is to look at Tumblr. There are many Star Trek fans on Tumblr who create and share fan works. Some might have written or reblogged fanfictions with this plot. You can search for relevant tags or ask the Star Trek fandom on Tumblr if they know of any such stories.
Sure. In some fanfictions, her pregnancy could be a result of a medical experiment gone wrong. Writers often use this situation to explore themes like motherhood in the midst of a space - faring adventure. The fanfictions may also show how the crew rallies around her, or how she has to balance her personal situation with her duties as captain, which makes for really engaging reads.
Archive of Our Own (AO3) is a great place to start. It has a large collection of Star Trek fanfictions, including ones about Captain Janeway being pregnant. You can search using relevant tags.
There's a fanfiction called 'Journey with Janeway and Seven' which is really good. It focuses on their adventures together and how they support each other. In this story, their unique personalities shine through as they face various challenges in the Star Trek universe.
One common theme is the exploration of their unspoken attraction. Since they were in a professional relationship on Voyager, a lot of fanfiction delves into the feelings they might have hidden beneath the surface.
Love and friendship are common themes as well. Some fanfictions explore a romantic relationship between them, while others focus on the deep friendship that develops over their shared experiences on Voyager. It's really interesting to see how different authors handle these relationships.