The bumps you're describing are flea allergy bites. It doesn't matter if you've never seen one on her, they don't live on the animal they jump on for a quick meal and then leave. Do you ever see flea eggs anywhere? Look around for tiny, little, hard black crumbs that would be wherever she sleeps such as on her bed or yours. You can test it even easier by giving her a white sheet to lay on tonight and check it out in the morning.
You're also giving her way too many unneccesary supplements, some which are known to cause allergic reactions such as scratching.... With Allergy dogs, flax and kelp is the worst.
Is your dog vaccinated regularly and fed kibble? Pretty much kills their immune system which is why she's attracting these things in the first place.