If you use Heartworm preventative, ask your vet to try her on Revolution for one month. Dogs can pick up mites that can be hard if not impossible to see on a skin scraping, and if it is mites, it will work noticibly within 24 hours. If that gives her relief, consider using it each month.
Another thing to consider is fleas. If she has a flea bite allergy, it doesn't take but one flea to set a dog off. If she's not on a flea product, Revolution takes care of them as well.
Also, I just learned recently that dogs can be allergic to dust mites, which are found everywhere, but especially in the bedroom, and especially in humid climates. As you said her itching is worse at night, this needs to be considered.
The Omega 3 supplement will help, but try giving her 1/4 to 1/2 the recommended amount, and gradually increase the dose. It may help her to tolerate it better. Coconut oil is also great for the skin, inside and outside.
https://www.revolution4dogs.com/default.aspx Dust mites cause common intradermal skin test reaction in dogs - DVM