I agree with Sue that if you are going to try aerating half the day, aerating at night makes the most sense. Have the aerators go off an hour or so after the sun comes up maybe? This is just my initial idea though. I also want to see what happens with aerating only during the day because that might work better for lakes that have algae problems. I can think of long-winded arguments to support both ideas, and I can see git1fiddle's idea working too. An important think to note when your lake depths get above 12' or so is that you can destratify temperature without destratifying oxygen if there is a lot of 'breathing' sediment down there. If temp isn't destratifying though, you can be sure that oxygen isn't either, so tracking temp is the number 1 place to start.
We can't be sure without testing, but I suspect we will find a part-time aeration solution that works. In my study I showed that you need to have that aeration running everyday, since things go south pretty quickly in these deep lakes, but part-time everyday is probably ok.
Ok, that's enough for now. My first forum post and I'm already long-winded. You should see my emails!