1. They have a working relationship with the employee. I believe it is safe to assume that as the employee is still working at the store, they are a relatively good employee. The manager has no relationship with you and it is normal to offer more benefit of doubt to the person you know rather than the person you don't know.
2. I'm sure that customers in the past have purchased items only to return them minus the accesory that they needed.
3. As the cartridges have been installed, the printer cannot be resold as is. Chances are the printer will simply be thrown out and if the employee wanted the cartridges, why not simply wait and take them before disposing of the printer? Why would they announce that the cartridges are missing?
4. Without solid proof, a manager isn't going to accuse an employee or customer of theft. As this is a low cost item, the manager would probably be even more hesitant to accuse a customer of theft without absolute proof.
You are making an issue out of nothing. Without absolute proof that a customer stole an item, a manager isn't going to accuse them of it and a store has more to lose by not refunding the money than they do by refunding it. The manager did the only thing that really could do.