There's 3 secrets in E1M1, you've found two. The one you are likely missing requires you to do backtracking and listen for a sound queue, there's a lift that lowers (temporarily but repeatable) when you walk pass the common entrance to the zig-zag acid room, the lift of which is located in another secret you've already found.
Basically, secrets are designed in 3 main key ways: Backtracking, oddities in the area (misaligned or different textures, broken patterns in the area, etc) and sound queues. There has been the odd timed or one time secret but that's incredibly rare. Rare enough to not even be worth wondering.
The automap only reveals secrets in one specific edge case, the computer area map (which will show unexplored areas in grey), and only if the secret is designed to show up in the first place. Otherwise, secrets are typically hidden (behind false walls marked as red in the automap like normal walls) or seemingly inaccessible areas.
As for understanding the automap, it has 3 main colours: Red, yellow and brown. Red are walls, yellow are ceilings with different elevation, and brown are floors with different elevation. The automap only shows lines you've seen, and only updates while you aren't looking at it (so moving around while in the autmap won't reveal new lines).
