If pregnant women are not allowed to work/live in radiation areas, and a submarine is one giant radiation area (even the non-nuclear engineering sections are considered low radiation areas on boomers at least), then they must be removed from the submarine as soon as it is found out they are pregnant. When you are on a Boomer, hiding in the middle of nowhere, this does not give very many options to remove said member, especially if the rest of the boats on your rotation are either broken, or no where close to being able to relieve you of a duty that MUST be covered 100% of the time. I have seen a death of a wife withheld from an individual until we returned to port one month later, because of manning and issues concerning getting him off the boat since no one could relieve us.
I am not saying women should NOT be on submarines, I am just stating that with women, there will be pregnancies, and to prevent the "sex underway" issue from cropping up again, I will assume that these happen when the boat is in port. You can say that these candidates will be "smarter and more dedicated" but as we know, "accidents" happen, and the fact is as an enlisted female, you may be stationed on a submarine for almost five years straight, during these five years, you will effectively go out for 3-5 months and come back for 3-5 months, then rinse and repeat for the entire five years. This in fact will not allow a female submariner to choose to start a family without ultimately deciding to choose herself/family before her job/mission. The option there is to tell female submarines on Boomers that they are not allowed to start a family, in which you now have an inequality since male submarines are able to start families of their own.
You also have issues of being short on manning, which are already issues without pregnancies. I have talked to a few women about this, because ultimately logistics will be figured out in the Navy in regards to submarines, however I see pregnancies as a huge issue that has very few solutions. Many of them (including my wife) say that the Navy should say "getting pregnant while at a sea going submarine command is not allowed", however I am not too sure how this measure would ultimately be felt by the vast majority of women (submariners and civilians alike).
Before I get any "hate" bashing, I am not against women going on submarines, other nations do it, and I think it is a necessary course of action that will help with manning issues on submarines and hopefully inject some more of the "best and the brightest". I however have been looking for any country that allows women to serve on nuclear submarines instead of diesel-electric submarines, which we do not have. As far as I can tell the nations that allow women on submarines are all diesel-electric submarines, in which being pregnant, unless there are complications or near pregnancy, are a non issue.
I am sure someone way smarter than me has already thought of these issues, but as it stands I see nothing in place to completely prevent someone from finding out they are pregnant while underway and therefore IT WILL be an issue. As with everything else I am sure it will get fixed in the big scheme of things, but as someone who slept 4 hours a day, 7 days a week, for 3-5 months straight every time I was underway, and that was AT manning, I do not feel envious of what some of my fellow submariners will have to go through and I hope we will be able to continue to maintain our mission throughout any additional unforeseen incidents that we were able to overcome in the past.