I personally have never noticed a difference between the two, but there are many BNers who find that the different ways of application do indeed change the scent, or at least some part of it. Another case of "it does for some, but not for others" by the sounds of it.
As for whether it matters - well, do whichever one you personally prefer I guess. I prefer sprays, but only because I think that there's an element of waste attached applying by hand. There are plenty of people who prefer the older style splash/shaker/dabber bottles and methods of applying.