I agree with Doris and Marda.
If she's happy enough, I wouldn't go in - I'd wait and see if she settles down by herself .. and encourage this.
I have a child with allergies, and my husband (and family) have them.
I am not fully understanding what you are saying about the coughing and drainage either.
My kids do get post nasal drip (with allergies, and also with colds) that will tickle their throat as it collects while laying down, in the back of their throats. Allergy meds DO help this, but my child is older. They take a night time allergy medication for this (actually makes them drowsy). This was all checked out and recommended for my child by doctor and pharmacist. You want to be sure the medication is suitable for your child.
I'm guessing you did all this but just wanted to mention it.
Some allergy meds (day time ones) can potentially cause your child to be hyper. So that's the reason I mention the daytime vs. nighttime varieties.
Decongestants can be helpful but are not typically recommended any more for infants. I do know some doctors and pharmacists recommend allergy meds instead as they will *dry* out some of the fluids caused by allergies (watery eyes, extra nasal runniness, etc.). Again - doctor will advise.
So .. that's what I would check first - are the meds maybe making her wake.
Good luck :)
** Raising head (by elevating mattress, etc.) can help with coughs/runny nose at night too (be careful with pillows where she is young), and also vaporizers - can moisturize airways and keep them flowing.