How to Avoid Areated Emulsions

1. Make More:
When using a homogenizer or stick blender, you want to make sure that you are making enough so that the head of the homogenizer or stick blender can be more than submerged. This usually means 200 to 300 grams for a stick blender. If it was not enough then it is just going to be sucking in air. The homogenizer that I have I can make as low as 100 grams. I used to really only want to make small batches. That was until I realized how much work, for one, and you need enough for pH and stability testing.
2. Tap Before You Blend:
When you lower down you stick blender or homogenizer, make sure to tap out the air before you blend. Otherwise, you will be pumping air into the formulation. You also want to be careful as you are blending as well. You do not want to be moving it up and down a lot. If you stop blending and re-put it in, make sure to tap it again. 
3. Make Sure you are not over blending:
Homogenizer or stick blenders, really should not be run for a long time anyway. For stick blenders, I recommend 3-5 minutes. For homogenizers, I recommend 1-3 minutes max. Of course test this and see the stability of your emulsion. The whole point of using a high shear mixer is to get the particle size small.
Can you fix aerated emulsions?
It really depends on your formulation. If you formulation has a high amount of a gelling agent that is good at suspending (like 0.50% xanthan gum) it is going to be really hard to get it out. If you do not have any gums or other rheology modifiers then the air will settle out over a day. Just make sure to stir out the air.