You may want to find another allergist - my son was tested at 7 months for his allergies which include dustmites. Now having said that, unfortunately most test results are not 100% correct (even after the age of 3). True exposure is the only test.
Since your daughter is coughing mainly at night, it sounds like it could more than likely be dustmites. First, you may want to hold off on the humidifier because that will cause them to multiply. These are the suggestions my allergist recommended to us and we know from experience with my husband, it truly helps
-Try to keep the temperature at 70 or below in summer
-Invest in allergy covers for the mattress - don't forget to cover the box spring in plastic as well. Also get allergy covers for the pillow (we actually have a regular pillow, covered with a plastic cover and then covered with allergy cover for my son in case of accidents).
-Wash all bedding in very hot water - you will probably need to turn up your hot water heater to 130 degrees at a minimum (we change bedding every other day and do all bedding for the week one morning). As soon as the last load is in the dryer, I turn down the water heater again.
-Curtains are also a big culprit of dustmites. We have eliminated the curtains and use roller shades instead. If you can't do that, I would try to wash the curtains as often as possible.
-I know that you can't always keep children from their stuffed animals, however they are carriers. Placing them in a plastic bag in the freezer for 24 hours is supposed to kill the dustmites. My ds has two that he sleeps with, we take away one at a time.
-Carpet - the best suggestion is to remove it if at all possible. Since you are in the testing process now though, you may want to try to steam clean (preferably with a professionally rented machine as they actually heat up the water) using an allergen reducer shampoo. Febreeze also makes an allergen reducing spray, but it is a little too fragrant for us.
Does it seem like a lot to do? It is, I'm sorry. It has become second nature to me though. Since we have started following the suggestions, ds has not had to use allergy meds and my dh has cut back on his drastically (not to mention his snoring has been reduced greatly!)