I had a very large dog who was fearful of lightning and would find the tiniest place he could hide his head in. Thankfully, living in El Paso we don't see much rain or lightning. She seemed fine once the lightning ceased. Sadly we just had to put her down at 14, but she never did outgrow it. I guess it wouldn't hurt trying a homeopathic remedy, but if I was you I would just comfort and hold her and put a blanket over her head.
My 4 pound Yorkie on the other hand is not afraid of anything. I know when he was just a puppy I worried about the vacuum scaring him - oh no, he just hopped on top for the ride!
