I really love their friendship too and they do still keep in touch, even though they don't get to see each other much nowadays because they live in different cities and David is busy with his new show, but they still text each other sometimes
this is what Emily said about her friendship with David and the other casts:
I love the fact that David treated Emily as an equal, he really has a lot of respect for Emily and really treated her so well and was so supportive and caring towards her while they worked on Bones together