Sam: She’s struggling.
Dean: How do you know?
Sam: Years of experience.

It makes perfect sense to me that Sam could read what Mary was feeling so easily. She’s so much like Dean and Sam has been studying Dean his whole life. He could teach the master class on Dean Winchester. Be an adjunct professor. Write scholarly publications and have them evaluated by his peers. So of course he knows that she’s having a hard time before Dean does. Because a lot of the time Sam knows Dean better than Dean knows Dean and he’s certainly seen Dean do the “bury yourself in hunting and ignore the pain until it goes away” thing a hundred times before.