OK, I've done more research on the maps and I've found some very interesting stuff.
Several of the maps have large Lo Wangs with different pallets just standing around. It's clear they're supposed to be some sort of enemy, but they don't do anything and you can't kill them.
However, there's one giant clue that points to what the Lo Wangs were supposed to be. Look at the colors used by the ninjas on the images below:
Don't they seem very familiar? The blue one the blue vest one looks really close to the blue seen on most of the Lo Wangs, while the red ninja's color scheme matches the type of colors used on the red and grey Lo Wang. The only one that doesn’t have a beta ninja color counterpart is the Lo Wang with the green pants, but that could be a ninja variation that wasn't shown in screenshots.
Now, look at these two screenshots showing the same area. The first one is a pre-release screenshot, while the second one was taken in the Shadow Warrior beta:
Zoom into the pre-release image, and you'll see a beta ninja in the distance. However, the screenshot taken from the Shadow Warrior beta shows one of the large Lo Wangs. In addition, the beta ninja has a blue vest, while the Lo Wang has blue pants.
My theory is that the Lo Wangs are actually the old beta ninjas. The colors on the beta ninjas and the Lo Wangs are a good match. What's weird is that the ninjas from the final game are in the beta and work just fine. My theory is that the final ninjas were given a separate listing instead of making them overwrite the old beta ninjas. The old ninjas were then modified to the point where they couldn't do anything and their sprites were overwritten by the final Lo Wang sprites. I have no idea why they did this, because every other enemy in the unused maps that appears in the final are in the maps.
My second theory is that several of the maps in the prototype were already long obsolete when this beta was compiled. There are several things that hint this.
First off, the maps that look like they came from 1995 or early 1996 have no functioning doors nor switches. The only way to get past them is to use noclip. That's a big sign that things were rearranged internally after those maps were last worked on, but were never updated to use the new tags and the like. If they didn't care about continuing the maps, they wouldn't update the tags to make doors and switches work.
Second, the 1995 to early 1996-era maps have lots of floating“DELETE ME” signs or objects with “DELETE ME” on them. You can't interact with a vast majority of them, suggesting their code was already stripped from the game when this prototype was compiled. If they did intend to continue work on these maps, then those items would surely be removed.
Third, they never bothered to replace the old ninjas discussed above with the final ones.
Fourth, the maps that have locked doors don't have the Duke 3D/Shadow Warrior-style locks on them. Instead, it seems that the doors would act like Doom's; as soon as you had the key, you could open the door. No having to insert the key into the keyhole. Of course, since their tags are broken, it's impossible to figure this out for sure, but it seems to point that way because they have no locks for the player to use.
It seems that several of the maps were added to this prototype with no intention of putting them in the final game. It's possible that development for the Shadow Warrior shareware (which this is supposed to be a pre-release version of) split from an old version of Shadow Warrior, and therefore had maps that were stripped from the final version. When it came time to get the shareware version made, all they needed to do was remove the old maps and use the latest .exe and art instead of having to branch from the still-WIP full version.
One bit of interesting information is that there are maps from several stages of development hidden in the beta.
*The first stage consists of maps made for the old Shadow Warrior that was about temples and ruins. I've shown off some maps from these before.
*The second stage consists of early versions of maps that would appear in the final game, but still have some quirks from the old Shadow Warrior in them, such as the beta ninja placeholders and some of ruin and village textures used in areas you wouldn't expect them to be, such as in Unfriendly Sky's bar and Floating Fortress' dock. They don't have any DELETE MEs in them.
*The third stage consists of barebones layouts that have no enemies, but only have the final's objects in them. Two of them are prototypes for levels in the final game, but others don't appear at all.
*The fourth stage consists of pretty-close versions of maps that appear in the final game. These have the final ninjas and geography of the final levels, but have several different things in them. For example, the prototype has a mostly-complete version of Rising Son, but the door to the turret and bath is locked behind a Bronze key. The key is hidden in the Grenade Launcher secret area found at the start of the map.
*The fifth stage is the shareware levels you can access in the beta normally. These are the most complete maps in the beta.
That's the second part of my research. Still lots more to come!