Holy chicken coop, batman, this is the third time this has come up in a week
I don't think it's really a difficult concept and I'm somewhat surprised it's causing so many furrowed brows...
it depends entirely on the effect.
If I got you to choose a card, lost it back into the pack, then found it somewhere unexpected - inside a balloon, inside an egg, inside the gallbladder of a passing goat...
clearly an easy methodical conclusion for the spectator to jump to is that you made them choose the same card and pre-loaded a duplicate. Despite almost any incredible lengths you can go to for the relevation, if it
can be explained by a dupe and a force, it becomes just an exercise in "how did he physically get it into the egg", but of course, that's not magic, it's just a puzzle.
If you are claiming that their actual, unique, physical card transported itself into an egg, or was restored after it was ripped or burned etc - any effect which can be pretty much deflated by someone saying (or thinking), "well, obviously it's an identical card..." - is made more powerful if the card is a) signed or b) has a corner torn off that will later match. When people start wondering about magic ink, and start scratching at the signature and asking to see the pen, you're in a good position I feel.
If however it is a matter of the cards magically doing things that seem to defy explanation, like a triumph effect - well, that's not really made any clearer by the addition of a duplicate, is it? You select a card, it goes back into the deck, the cards are shuffled faces into backs and with a magical pass, they are all correctly orientated in an instant, except the selection... the idea "it must be a duplicate card" is fairly obviously redundant and absurd here.
With regard to your performance rvoice100, I don't actually think the card needs to be signed for In a Flash; whether or not the card that the "fire stops at" is literally the same card as they just handled is totally unimportant - the "magic" is in the fact that they're seeing something quite shocking happen (a coin wrapped in tissue burn through a deck of cards) and that this wild, uncontrollable force of fire is somehow magically influenced to extinguish itself in a way that reveals their selection. Again, the "it must be a duplicate" theory has no real bearing on a "solution" whatsoever.
Basically, magic in general and also the reputation of card cheats having extra aces up their sleeves means that even a spectator who is trying to cooperate will at some point end up thinking "I bet it's not really my card" if you give them the opportunity. Having a card signed eliminates this. Job done!
Of course, it also has the added benefits of saving you from embarrassment if your nervous or intoxicated spectator forgets what they selected, and makes the card a bit more personal should they want to keep it as as a souvenir. (I never force it upon them by the way... suggesting that everyone who sees a trick is a desperate to take home a grubby playing card with their own signature on it is a bit arrogant, not to mention the rate at which it depletes the deck, but if they ask that's another matter).
So in answer to your actual question - the issue of having some signed and some not should never really come up, because it should be obvious why you're having it signed for a certain effect.