I'm honestly surprised to learn they DO clean the balls; I somewhat assumed they would just throw the fouled ones away, and every once in awhile replace them all.
The more central to the business the more likely it is they have the dedicated cleaning equipment. It takes a fair amount of space so places like fast food restaurants are less likely to have one (but might use a service that comes by with one too).
Those balls are pretty expensive when you consider the volume needed. When my brother made his ball pit it ended up being more expensive than a nice couch. I think the price for the crush-resistant type at the time (~2007-2008) was around $0.20-0.25 per ball.