We've done several Ghost Brackets on Fatboy's in our shop. I had them on my old Dyna as well.
They are a pretty slick set-up and will work with most all saddle bags. There is a metal plate with the Ghost Brackets that you mount to the backside of the bags, so they fit everything out there. As far as the fender struts, you should be OK. Be aware, that you will most likely have to relocate the rear turnsignals. There are several kits out there to move the signals rearward allowing enough room for the bags.
Taking the bags on and off is a snap and the only visible evidence left is the grooved bolt heads on the fender struts. I believe the new models even have a lock to keep the bags from walking off.