One reason shops might refuse to take large notes is the ability to give change. Tills usually have less than 300 euro in the drawer and a time lock on the safe change needs to be kept to serve other customers.
Rather than refusing, I often ask customers when would they would like to call back for their change. At that stage they usually come up with an alternative method of payment.
But I am familiar with the security features of large notes. Younger staff might not have any experience of handling real large denomination notes. And they can be held responsible if they accept fake notes without authorisation.