It can get tiresome, but only if you breed in large numbers and don't sell as much. Luckily my last spawn, every one of them was sold fast, 98% of them the first day they were listed. I personally use 3 airline hoses held together by plastic zipper ties and will go through each beanie (not moving them) and siphon out 90% of the water with it - collecting the waste as well. It drains pretty quick.. hold a finger on the opposite end of the airlines and move to the next beanie. I will do a thorough cleaning of the containers about twice a month using those sponge paint brushes, but I do daily water changes.
I know others who just set up a folding table near the sink and will fill up a couple empty containers and start the transfer/cleaning that way.
But like mentioned above, it does depend on how big of a breeding program you run and whether or not you have an outlet for your unsold fish (I have a wholeseller that takes them off my hand for 50% profit, which is more than I would get from a LFS). Luckily, haven't needed to use him yet, but that's an option for me to help keep the numbers down to a reasonable amount. So definitely look into that as well - finding an alternative place to take the ones you don't sell - so you don't have as many to clean.