DarknessConcept: So I was thinking about this again and decided to jump in and see. I loaded up E1M1 on the easiest setting and ran through it. I was mis-remembering about the spawn point in the dumpsters. One trooper did spawn as I neared the dumpster, but none appeared as I entered it. Also, I finished with 24 kills and the stats screen said I left 1 enemy remaining (25 enemies total).
Shieru-sensei: Thanks for trying that out! It's kind of a bummer, though, as I don't exactly know when and where these enemies spawn. I wanted to play through the game with 100% kills like in Doom.
This video shows a secrets / kills counter at the top of the screen. I've asked the uploader how they enabled this feature so if I get a response I'll let you know!
EDIT:
Noteworthy: you'll notice that at the start of the video, the kill counter read 33 enemies. As the player progresses through the level, enemies spawn in a few different areas which makes the total increase (mission ended on 39/39 kills). So, if you could enable this feature yourself, you'd just have to make sure you had all kills (level base + any that may have spawned) before exiting the level. It appears however that you will have no way of knowing if you have triggered all possible spawn points. For instance, If the player in the video had avoided the dumpster that I mentioned, the lone trooper would not have spawned. They then would have been able to exit E1M1 with 38/38 kills which is technically 100% kills. In any case, I think this would be a useful feature for you. Hopefully it isn't a Megaton Edition (Steam) exclusive.