I've read and heard comments from people saying you are supposed to exclude all Supply Deck cards with the Valuable trait when playing LotA. If I recall correctly, even the boardwars guys said this before (I believe during one of their LoTA playthrough videos on Twitch / Youtube, but maybe on the podcast too).

Is this correct though?

In the LotA rules (page 4) I can only see that it says to remove certain valuable cards: Valuable Goods, Troop Data, CI comlink, Chance Cubes and Pit Droid.

Is it fine to use other Valuable supply cards such as the Missing Key, Locked Chest, Supply Chest, etc?

I think they’re making a generalization. The app is incapable of recognizing the excluded cards. So the Supply Chest is definitely acceptable.

As for the other two, the game can’t recognize if you have the reward. The rule book’s last update seemed geared to this expansion so I think you’re okay to use them.

Yeah, Stephan overgeneralized. Not all Valuables are removed, just the ones dealing with credits.

There hasn't been an update since August, so Missing Key and Locked Chest might be added to the LotA rules at some point, but the Hondo's Treasure reward isn't too powerful, so it doesn't matter that much if you get it for the final (it's unlikely to get it at all during an app campaign).