While I will agree that if they're done poorly, they aren't worth much more than a potato, if done correctly, you can never tell. Here's mine, it was a longbed and the only thing that clues one in is the boxing I added behind the crossmember. Other than that, you couldn't tell it's been shortened.
I've seen plenty of cars that have sold for good money that had IFS clips scabbed on and other sketchy frame mods so I'll never understand why this long vs. short argument persists. If it's a case of original equipment, that's a different story, but I don't run with the restoration guys, they get a little weird when it comes to changing fuses, let alone actually modifying something to make it better...lol.
Cody Wentz's truck used to be a longbed. Bet you couldn't tell...
I guess it's up to the buyer, a junk truck is a junk truck, regardless of whether it's long or short. But the shortbed would definitely bring more cash.