Pac-Man ghosts appear only in secret levels, and those levels are not awarded individual level stats (presumably at least partly because two of them have no secrets and nobody wants to get into a 0/0 debate) and do not count for the episode stats. If you MapEdit a ghost into a non-secret level it will count against you if you don't kill it.

It's reasonable to suggest that 100%ing an episode should include 100%ing its secret level where possible; 100%ing everything else then straight rushing the secret level because it doesn't count towards the end of episode stats seems nonsensical. Of course, this is very difficult to track, but knowing how many points are available on a level and how many secrets there are provides a check. (For example, E3M10 has 180000 points available, which means if you've got 179500 then you've missed a chalice somewhere; or E4M10 has 75 officers, which give up 400 points each for a total of 30000, so I hide in the level's one secret and blindfire into the dust until I've got 29600, then I know the last guy is jammed by the lift. This counting strategy doesn't always work, as extra lives count as treasure for stats but award no points.)

In DOSBox Wolf3D at least, IGT doesn't account for boss (or secret) levels.

Technically the fastest way to move is (I think) keyboard, mouse, run and strafe together - remember you can't turn and strafe together though (on the OG at least).

Testing with DOSBox confirms that you can mouserun faster by increasing the mouse sensitivity.

A few reasons come to mind:

1. Nobody wants to. It's not considered as technically impressive to kill and find everything (which is a test of memory as much as anything else) as it is to mouserun everywhere and skip all the keys.
2. It's hard. E4M10 and the E5M2 gauntlet come to mind immediately as just straight-up brick walls for a 100% run, and how much hair are you going to lose if you miss one chalice on E6M8?
3. It's not always possible. E2M8 is literally un-100%able (I'm not certain but E6M10 might be as well, ignoring the invincible enemy issue that also affects E3M10) and port/engine issues with the 3-square pushwall bug ruin at least four more levels and slow down several more. (I'm looking at building a Windows 95/8 era machine for authentic OG DOS runs to deal with this, but... yeah.)
4. Timing. DOS Wolf3D ingame times and statistics don't account for the secret or boss levels, and timing manually is subject to the vagaries of loads.
5. Categorisation. I've 100%d E3 IADI in under 25 minutes (realtime - can be done a bit faster) before but there's no 100% category, and who wants to post a 24 minute time on a leaderboard where the record is 3 minutes?