If you play your kick fairly unmuffled it can make a difference I find.
There's a noticeable difference when you play a non-virgin bass with nothing mounted on it.
I find they usually have a bit more sustain and are much boomy-er.
With lots of heavy hardware mounted on top it can kill the sustain quite a bit though, I suppose it's because you're adding weight to the shell, and that makes it resonate less.
But yes, if you muffle your kick heavily, the difference is only in options of drum placement.