To answer your question in short, I would fill only the mesh pot. The airspace left in the 5 gallon bucket will stay very humid as it is sealed off from light and most airflow. So when your solution drains, the roots will be dangling out of the mesh pot filled with hydroton, into a very humid air... which I would say sounds good to me as it will keep them moist but allow some air contact as well.

You're using ebb & flow with 5 gallon buckets and mesh pots? Interesting setup.

If you fill the whole bucket with hydroton, you do not need the mesh pots on top and can just plant your prize in the bucket with pebbles. Most people who use the mesh pot and a 5 gallon bucket are rocking the DWC setup. In that setup, they would fill only the mesh pot with pebbles and the bucket would be filled with nutrient solution up to the bottom of the mesh pot.

Since you have everything but (presumably) the air pump/stone, I would give DWC a good look-through. It's a very productive growing method and you already have most of the requisite parts.