I've been thinking on this a lot and trying to analyze what I feel in my gut about ignoring a frightened pup. I know that I try not to make a fuss and coddle lest the dog sees that I'm worried to. But I don't think it's natural to completely withhold any attention or sympathy from the animal. I mean....the dog is very afraid of the loud noises and then on top of it, his mom is completely ignoring him? "That is something she never does to me and now, just when this super scary noise is happening, she doesn't like me either." It's not normal to ignore the dog. I mean...usually you don't ignore your dog, right? Unless, of course, there's some rotten behavior you don't want to perpetuate. But this is not like your dog is doing something on purpose. He can't help it. So all of a sudden there's this weird reaction (or non reaction) associated with the thunder. Now you've got a double dose of weird, scariness. The thunder and a silent Mom.
So, with something my dogs are afraid of or alarmed about, I usually say something like, "It's ok, it's nothing" in kind of a sing songy, care free type voice. I acknowlege that I'm aware of the thunder (or whatever) and that the dog heard it, but I try to get it across that although it's loud, nothing horrible is going to come of it. (I do that with my voice.) Can you believe me? LOL. I don't hover or act like something is super horrible and inadvertantly tell the dog that his fear is going to get him a neurotic amount of attention. LOL. Just a little bit. I have noticed my dogs look like they believe me and settle down a little bit...relax. I know this is an extreme fear your dogs seem to have, but I don't think a complete ingoring of them is a good idea. Just try to portray an attitude that you're confident, you're not worried, things are going along as normal, there can be a game, some treats for a sit or roll over trick....try distracting them a little. And play Bach. LOL.