See, that's the key right there - get the deck signed IF and only IF it will have value TO YOU. Forget the future generations, forget they guy you're going to sell it to on eBay. If YOU value it, get it.
On the one hand, paying extra for a signature does sound a little silly. But then again, when you're juggling a project's fulfillment as a one-man show, it does indeed cost some time and effort, so asking a little bit extra for it isn't beyond the pale. If it's a one-man operation, yes, that is a hassle, but you want to make fans happy. If you're using a fulfillment center, there's the logistics of getting the decks to you, signing them, getting them to the center, then having the center send them out (or perhaps you send them yourself) - so no matter what, it's not a quick process, particularly if you have many requests for autographs on top of all those Customs forms that need to be dealt with!
It's simply a matter of how much extra - a buck sits well enough with me (assuming I was the type to seek out signatures, which I'm not). More, only if you're really famous and have a product I want - I've paid extra for David Blaine autographed decks because I wanted the decks and they were otherwise unavailable.
I prefer autographs that I obtained in person - those have meaning to me. No monetary value - but meaning, sure. There's a difference...
I'm not even going to touch the entire "on the box or on the cellophane" debate...