I can only speak from pulling kids in kid trailers or one wheeled bikes. Specifically iwth trailers, Ive pulled them with both a steel framed touring bike and an alu framed mtn bike that has a much stiffer rear end of frame. Cant really say Ive noticed a diff, as the main feeling I recall is the push/pull of a trailer. Others may have diff experiences but Id have to say given the diff characteristics of my two bikes pulling stuff, I cant really say there is much of a difference. (mind you, Ive never done a back to back test, this is just from recollections)

i suspect the difference with a stiffer bike is always going to be how with hard pedalling, a stiffer frame will not have the "give" of a softer frame. Pulling stuff or not, but one will be working harder with pulling something as opposed to unloaded, so one will feel this effect in any case, trailer or panniers.