*canceled*

I did the quest 2 times without Letho (I killed him for trying to frame Geralt in W2). I got 2 keys one opened the barn the other opened the the box below the message (I got that key from Delores).

The only thing I can think of then, is that I didn't notice the locked location at the time and missed it, then proceeded in the game to a change point that made the loot no longer available, or perhaps I did actually get it and it is empty already. In that case the game isn't providing me feedback to know with certainty either way. For example, it says that it is locked, and if I had unlocked it then the game should not say locked anymore. Hard to know what the truth is though. :)

Do you know what the name of the key is? I still have all of the keys I've ever got in the game unless the game removed them on its own from my inventory.

Sounds like another bug to me. If I remember correctly I played the quest before 1.06. You should probably wait for 1.07 and try again. You may even load a save game before starting the quest.
But sure it isn't linked to if Letho is or isn't present in TW3.

Just to be sure: http://www.vg247.com/2015/05/18/the-witcher-3-the-fall-of-the-house-of-reardon-walkthrough/

"You need to fight a handful of Wraiths that shouldn’t put up too much of a fight. In one of the smaller buildings nearby you’ll find a small box that gives up the key to the big barn. It’s inside the barn (there’s a side door to the left of the building) that you’ll find a chest with some money in it. Now just return to the old lass and you’ve done."

When you complete the quest by returning to Delores in Lindenvale, she asks you about the money in that chest. Says it's your payment for getting rid of the wraiths.

But like I said, if there is no key for that stash at all, my bet it's a game bug. There are actually all sort of quest related bugs and I know first hand that "missing keys" is one of 'em.

I can't be 100% certain I didn't already do it, but I don't remember doing it and I haven't encountered many things in the game that my memory is fuzzy on so I'm inclined to believe I didn't do it. I have encountered some key related bugs as you suggest though, one in the ancient cave where the sunstone is found and there is a locked chest with no key to be found. I did some searching and people have hacked through the game's data files to find that there is a key but no way to obtain it or something like that. :)

So I think you're right, it's either a game bug, or a memory lapse on my part. Either is plausible but I'll do my best to unlock the missed out on content in the next playthrough I do. :)

SPOILERS*********

To recap - At the end of W2, you make a choice to kill Letho (who is a boss villain and also a witcher, IIRC from the viper school) or let him go free. If you let him go free, he shows up in Delores's estate which Geralt finds booby trapped that you can disarm, and there is a questline that follows. There is also a timed decision in that questline to "interfere" or do nothing to stop Letho from being beheaded. If you do nothing, Geralt talks Letho's enemy into simply taking Letho's medallion instead of his head. If you interfere, you must kill the boss and his minions. Either way, Letho was not really dead but only appeared dead due to a poison/sleeping potion, and the questline ends with Geralt suggesting Letho hide out in Kaer Morhen. This sets up Letho to be included for the Battle of Kaer Morhen later in the game.

You will also have a chance to send other NPCs to Kaer Morhen, for their safety at the time, who become "allies" at the battle. There's also an achievement for a "Full Crew". Some "friends" by default feel they cannot go to the battle, much as they might want to help Geralt. Apparently, they are not part of the "Full Crew".

Delores gives you the key to the hidden chest (Geralt's pay) when she gives you the quest (Fall of the House of Rearden). You find another key in the house for the barn. The hidden chest is next to the "Delores" written on the wall in the barn. I'm pretty sure that once a locked chest is opened, it can no longer be opened if you emptied it.

If you didn't play W2, or you did but killed Letho, he won't appear at Delores's, you don't get his questline, and he won't be at the Battle of Kaer Morhen. Instead, Geralt finds wraiths, just as Delores told you. Yes, when starting a "new game" on the opening menu, you have a choice to "simulate a witcher 2 save" or import a witcher 2 save. When you simulate a witcher 2 save, you are interrogated by Voorhis at the Emries' castle in Vizima - the shaving scene - where you can choose whether to kill Letho or free him and other decisions. Dunno what happens if you chose neither though. *I think* you don't get Letho at all and the shaving scene, there is no interrogation apparently.

FYI - Though it might be confusing and if you never played W2, you can google search what W2 endings/decisions impact W3.

I get rid of keys as soon after they move from quest to "other".

First time I did the quest, I had "cleared" the Manor of wraiths, then found the quest in Lindenvale, talked to Delores (in Lindenvale) about the quest and she gave me a key. Next, I fast traveled to Reardon, unlocked box, got reward, fast traveled to Lindenvale, told Delores Manor was wraith free to finish quest. After that I went through the Manor going to explore "?" in the NE and I think I saw Delores there.

If you have not done so already, you could check in completed quests to see if you did complete the quest. Maybe this is one of those quests we are warned about that cannot be competed after Kaer Mohren.

As Letho can be sent to Kaer Modren, this maybe true.