I feel that "Thank you for the lovely card and gift" or even just "Thank you for the gift" (because the giver knows the card got there if the money did) are best. Like your mother, if I received the thank you note she did, I would wonder if the card had been tampered with, or if I'd forgotten to include the money, as mentioned in an above post.
Of course, she should have asked your daughter this directly via email or phone. You should not have been put in the middle since she is old enough to answer the question herself and since, as you said, you don't even know the answer. But, since it's been done, I do think it would be good to casually mention to your daughter that her grandmother was concerned that the money might be missing.
If she did receive it, she can send her an upbeat email like, "Hi, Grandma. I heard you were wondering whether I'd received the money you and Grandpa sent in the card. I did! I'm sorry I forgot to mention it! Thank you!"
And, if it was missing, she can let her know that, too, and that she doesn't expect her to replace it (or send it for the first time).
It was mentioned that it can be awkward or considered crass to mention receiving money, which is true, but it is considered perfectly polite to refer to it as a "gift."
ETA: I do understand how your mother might have thought it was better to ask you, thinking you might know the answer. She may have thought your daughter might feel like she was criticizing her if she asked her directly.