My dd 3 has allergies and asthma, and we ALWAYS give her sudafed about 30 minutes before a flight takes off (right before boarding). We also have lil' noses which is a saline spray, if she is really clogged. These were recommended by our ENT and asthma specialist.
The sudafed is non-drowsy. We also have a sippy cup with us, and usually a bottle of water that we can transfer to the sippy cup if she drinks all of it. We give her that on takeoff and landing.(We put her in pull-ups then too, because she is scared of the stainless steel toilet in the airplane.)
We have also had starburst and skittles that we have given her if she is not thirsty and will not drink. They are messy at that age, but we have not had any problems.
Good Luck.