It seems very likely that your wife is correct about what happened. Whether she is correct or not, keep a very, very safe distance from her mother.
Your plan to write thank you cards to all who attended is an excellent one.
If you do uncover from some of your close friends that they gave a card you never received, then you can be pretty sure that you will indeed accidentally offend someone by not thanking them for their generosity. In your shoes, I guess I would address it at that point by contacting each person (in person, phone, whatever) to thank them again for coming to the wedding. Tell them how grateful you both are that they shared your special day with them. You could tell them how you enjoyed your honeymoon, how much fun you had dancing with them at the wedding (or whatever), and then mention that a crazy thing happened: it seems a few people gave cards that definitely went missing . . . I would then probably downplay it with "they say something always "goes wrong" on wedding day, so I guess that is what went wrong on ours? Everything else was perfect! I'm so glad you were there!")
That gives the other person an opening to say "I was wondering why you never cashed my check!" or "Oh no! That's terrible! Please tell me my card wasn't stolen! I put something in there for you!" Then you can say "Oh dear! I guess it was! I'm so sorry that happened, and I wish we had had a better system for keeping an eye on the gift table. Live and learn, I guess, but who knew someone could do something like that? It's a mystery, but the main thing is that we are very happy you were able to join us that day. Thanks again!"
You pretty much know who did it, but I wouldn't blame anyone publicly . . . I'd just call it "The Mystery of the Missing Cards." If someone presses you about it, asks you who you think took them, you can just keep repeating "We don't know. I guess it's just the Mystery of the Missing Cards." That's what we did when our pet toad disappeared. My son was fairly sure one particular friend stole it, and he could be right based upon all the other things that "friend" did, but I knew we couldn't be sure because a couple of other people had been through his room (like other friends and an apartment maintenance guy, although it seemed very odd he would have taken an amphibian). I also knew it was possible the toad had suddenly learned to climb the glass wall and somehow escaped out of the blue despite the lid. I told him we'd never know, and that he shouldn't accuse his "friend", and that he should stop trying to solve it in his head. We agreed to just call it "The Mystery of the Toad." Once we named it that way, he stopped being so upset, felt better, and could just let it go. The toad never appeared (dead or alive.) It remains a mystery to this day.