The resonant frequency of the boards is the same, but a vibration will have to be stronger to get through a 3" than a 2" board.
I have used stands with MDF shelves. It worked just okay, then I changed to 2" maple, there was an improvement, then I changed to 3", and again it was a little better. THEN I changed to a Sistrum all metal rack and have never looked back. It was better in every way...
I know there are better racks, but they cost a lot more, I'm trying to squeeze out the most music for the least amount of money... call me cheap, or call me Ahab...
:o