Can we get an official response for the missing DLC?

I upgraded to Deluxe about a week ago, and those specific items did not spawn inside a chest (like the N7 do, as soon as you return to the Lighthouse after recovering the lyrium dagger, or the Blood Dragon armours); instead, you get successive pop-ups at the bottom right part of your screen for each of the Deluxe Edition items added, and that occurs retroactively to each save you boot up in my case.

Did you try uninstalling/re-installing the game files?