Congrats women warriors!
Only 2 potential issues I see.
1. As Kaolin said, women tend to require separate facilities and more personal supplies (yes a year worth of pads for each woman on a sub could be a big deal when space is tight), this is a big problem for a Sub and, if it effects efficiency, should prevent women from serving on them. If you can get around this issue (put em all on depo shots, and they have to use the same facilities/bunks as the men) then there is no reason women shouldn't be allowed to serve on a sub. I don't have numbers and I've never been on a sub, so perhaps this isn't an issue at all.
2. Men are more likely to save a woman in danger than a man. Now, you may say, "so what" and normally I would care less which person was saved as 1=1, but in an emergency situation on a sub a man having to choose between say, locking a bulkhead immediately, or waiting for someone to get through is more likely to wait, endangering the rest of the ship, if there are women on the other side of that bulkhead.
Men tend to be hardwired to protect women more so than other men, so having women present changes how we make decisions, it changes the weight on our pros/cons scale. This can be very bad in situations where hard, fast decisions with life and death consequences have to be made. I can't see a way around this in any integrated situation so really there just needs to be some good studies to figure out whether this is more of a pro or a con for efficiency. Maybe they've already been done, anyone read any?
Disclaimer: All submarine knowledge was gleaned from "The Hunt for Red October" and the sandwich shop down the street.