As many people with allergies will tell you - they can get worse if you keep getting in contact with the triggers. Also, allergies or intolerances can develop later in life and don't have to be a 'from birth to death' thing. Some cats can be intolerant or allergic when it comes to grains, potatoes, certain types of protein or the specific thickener that is being used for some wet foods. So yes, allergy might be an option.
When a cat has sores or scratches itself, there are generally these common causes:
- Parasites (you accounted for that)
- Fungus - I assume the vet took a sample from the wounds to check for that? If not, have him do so of course.
- Food allergies. I think this might be most likely right now.
There are allergy tests for cats, but they tend to be unreliable at best, so usually it is advised to test giving pure raw meat to the cat for a while - preferrably a protein it hasn't eaten before, for example horse or goat. This is done for about 4 weeks at least in order to make sure that the immune system of the cat had time to calm down, so to speak.
(Preferably, the meat should be fed with a pinch of salt, some blood and a pinch of powdered eggshells (for calcium) to there are at least -some- supplements)
If raw meat isn't an option for you, the only other possible way to do this is feed mono-protein wet food without any grains whatsoever. So for example a wet food with only horse ingredients and ~4 percent of carrots/pumpkin should be fine. No grains, no potatoes!
The ingredient list should read f.e.
95% Horse (50% Horsemeat, 20% Horseliver, 20% Horseheart, 5% Horsekidneys, 5% Horsestomachs), 5% Carrots.
(and of course calcium, phosphate, taurin etc.) Meaning absolutely no unknown ingredients.
As you start the diet, you can ask your vet to help alleviate your cats symptoms temporarily (only if they are really bad as its not like he will give her sugarpills and all that) by prescribing cortisone. Cortisone is an immune supressant (among other things) and will therefore suppress the reaction of the cats body. Its heavy medication though and should not be given (or stopped) lightly.
If the diet proves that your cat does have food allergy, you can slowly (as in - 1 per month) introduce 1 new ingredient/protein at a time. This will help you figure out what exactly she reacts to (there may be multiple things) and adjust her diet accordingly.
Dry food, by the way, is most commonly a no for allergic/intolerant cats - grains are notorious for that and dry food is just factually mostly made out of that. (and therefore is more suited for chickens than carnivores anyway)