There are quite a few Underwater Futurepack Air Domes that really seem to serve no real purpose. The broken water flowing is creating unnecessary lag and I want to greatly reduce or turn off the generation of these domes. I did not see this option in the configs... am I missing something?

can you make a screenshot? because I dont know what you mean.

And on wich Minecraft version are you playing ?

Ran into this too. It appears the world gen appears to attempt to generate the crystal domes in ocean biomes, creating large air pockets of flowing water and crystal. The water is in a "frozen" state, however an block update floods the "dome".

Are the completly inside the ocean or only the upper part ?

In my experience they spawned on top of the ocean floor. However the big crystal expand upwards and so does the air "dome".

Ahh yeah, detected this is harded then it sounds, because checking to much blocks can cause generation of new blocks, but iw will try to avoid this.

This will be fixed in the next 1.12 version.