You shouldn't get to much vibration if any from the actual mounting point but the panel itself may resonate some and vibrate against other objects. What kind of speaker is it? If it's a subwoofer some kind of gasket is a good idea to keep a good seal.
Mount it solidly and make sure it is properly sealed will no gaps.
The key is to get the speaker to direct as much of the wave energy it produces into the air, as this is what produces the sound we hear.
If the speaker is mounted on energy asorbing material it will reduce the amount of sound waves that are emitted from the speaker, likewise if there are any gaps, air waves from behind the speaker can effect the air wave from the front of the speaker in a negative way.
The reason for using sound deadening material is to reduce the rattles from any panels that are vibrating. Go ahead and pad the panels as much as you like, but avoid doing anything to the speaker itself.
it depends mainly on the type of speaker that u are talking about.
With 6.5" splits, they are perfect in the factory position and giv hardly any rattles with no sound deadening. That also applies for 6x9s. With subs, u would definately need sound deadening in the boot lid and depending on how extreme u would wanna go putting sound deadening in the rear bumper and side panels would help as well.