Donkeys/Mules can be very protecting, yes they may try to get your dogs but like any animal if you work with it enough and get them used to your animals then it should be OK. They can be good guard animals just make sure you work with them.
I do not have a herd yet but I am looking forward to having one in the future mainly beef cattle, pigs, goats, and horses. I am looking forward to learning all that I can and as much as I can about herds.