As far as I can tell, this is more common in the US – I'd be quite surprised if Euronet depended on business owners to restock their machines rather than having their own couriers doing that.
But in either case, I don't see how a merchant could hide anything using an ATM: Dispensing $100 of cash via a self-operated ATM has exactly the same effect on their bank account as depositing $100 of cash directly at their bank, no?
Other than that, this would then not be any different from a regular cash deposit, no?