Shouldn't the female protagonists be pregnant?

They absolutely could be. The trouble PCs and their companions get into, getting knocked around by bandits and demons and darkspawn, not to mention all the hard traveling, you could easily headcanon a discrete miscarriage or two into any of the games.

Medieval-ish sexual mores and average medical knowledge considered, a fantasy heroine might catch and lose the baby early on, and never even realize she was pregnant in the first place. There's no 'going to the doctor' culture in Thedas outside Tevinter, except maybe among the more open-minded of the high nobility. Not everyone would feel comfortable letting a party healer like Anders or even Wynne examine them intimately intimately enough to say, no matter how many battle wounds they'd helped patch up.


I like the lyrium low sperm count theory. If lyrium is part of the Joining cocktail as well then that'd be one explanation for Warden infertility. Plus, Morrigan has a vested interest in no other warden babies interfering with her ritual in Origins, and might have taken some precautions on everyone else's behalf.  

Cullen and Blackwall are also both principled and disciplined enough to... uh... back out in the last minute. Can't imagine either of them taking that kind of risk if they thought it'd endanger anyone, including a potential child. Solas would at best have very mixed feelings about bringing a new elf/half-elf into the world as-is. And... do we know if Qunari can interbreed with humans, elves or dwarves? Iron Bull certainly doesn't strike me as seeing sex purely as a method of procreation, but in his situation there's plenty of reason to avoid complications.