If you're buying shocks made for your car by Acura, yes the transmission does affect the shocks a little bit.
The manual transmission is lighter than an automatic, so if you get front shocks from an auto TL, your front will sit higher than it's supposed to.
Many automatic TL guys who go with with the Acura A-Spec sport suspension prefer to find the manual variation as it allows the front to sit lower (looking better) as the auto transmission weighs more.
If you're going aftermarket, it doesn't matter because the companies don't get technical with the variations of the car.
PS: Our cars don't have struts.