I have discovered that "items" appear to be glasses of water, armor cans, and Supercharge Breakfasts. Based on this, I am led to believe that "items" are things that the Chex Warrior can always pick up. If this is the case, then why are zorchpaks (the gray ones), computer area maps, and keys excluded? Is this a bug?
Those are "powerups." I only use quotes because keys aren't really powerups. Backpacks, Maps, Soulspheres, and other powerups are supposed to be hidden, at least in the original Doom. They weren't counted in the item count, since the player might not find the secrets.
Ah, that makes sense. Perhaps it isn't a bug then. It is interesting though how some areas (such as the laboratory) have two of one of the keys. Perhaps it was meant to be similar to Commander Keen as well where, once used, the key was gone from the inventory and there is multiple doors of that color. The main area that I can think of for this is the Pyramid of Moons. There are two yellow doors. Although I think that there is only one yellow key to be found in the level. If there is a second key, I have not found it.