It sounds like you handled it really well

and the thank yous will get done eventually. I agree with recent posters that it really hasn't been that long and she could be waiting on photos, etc. (maybe even the ones which are "done" now are not sent yet waiting for a photo or whatnot). I would not question it before 3 months even when both newlyweds are home and certainly not from a bride who is stressed with a husband in a war zone (and yes please do thank your son from me and my family as well).
If anyone else asks you about their gifts and not receiving a note I would just smile and tell them you are sure she appreciates the gift but you have really not spoken to her about thank you notes as you two tend to be worrying about your son when together (gentle reminder that there are ore important things going on in her life).
Funny, I have two kids. I do make them send thank you notes or emails. Although--DH and his siblings got together a few years back and all agreed that verbal thank yous were all the kids needed to do with each other aunts/uncles (nice for OUR kids who both have birthdays Christmas week which makes for a lot of writing come early January). DD wirtes long, thoughful thank you notes. She ENJOYS doing it and still insists on sending them eve nto the cousins and aunts and uncles. DS has fine motor issues and writing
at all is a struggle for him. He always writes the bare minimum ("thank you for ______. I really like it. Love Rio

). I get photo cards for him to write on so it seems a little more real

He is very grateful and will tell you so profusly on the phone but he HATES to write (or even type) something and would truly rather just not get any gift at all. So, I can totally see him not sending thank yous some day when he gets married (or buying Scott's and Rob's program).