Your post reminds of years ago when we tried putting goldfish in the tank to clean it. The poor goldfish were gone the next day. We suspect that a clever raccoon went fishing.
And you’re absolutely right that many barns with outdoor troughs don’t clean them in the winter. The theory being that the cold keeps things from growing. True to some degree, but those things get nasty when horses poop in them, put their feet in them, dunk hay in them, etc.