There is no way Amy is pregnant because there is no way on this earth that TBBT would simply pass over Shamy having sex for the first time and just jump head first into a Shamy-baby.
The writers are smart. They know that Shamy is their power ship and they’ve shown time and time again that with this ship, the steps are small but significant and more to the point follows a logical course for the two characters that make up Shamy (hand holding, making her his emergency contact, the kiss, being scared of commitment, acknowledging that he’s scared of what Amy thinks about him, the I Love you, Mars, The Fort—it’s a clear path for them)
There is a very clear line of thought coming from the writers room about how to progress these two. Sudden baby (which would have meant sex) would be the equivalent of of jumping over several huge points.
Passing over and hand waving away coitus for the first time? Not going to happen.