Really interesting read this thread I had always thought you could 100% Quake. Duken Nukem is the same with the secrets in the PAL version you can't get 100%. I know a few missions where the secret doesn't trigger that you have it.
I was going to do a Duke 100% run but it doesnt have the nice feature that Quake Saturn has where you can pause and double check the kill/secret count. It just makes it so much easier to do.
The one thing I learned about Duke over time is that some of the secrets are even missing. My guess is they rushed through Duke to try and finish Quake to get it out for the deadline. Quake is overall more polished completeness wise. Im definitely not knocking Duke 3D. They did an amazing job. It just is what it is. For example there are a couple secrets where they forgot to add the powerups. Or the one in the sunken city. Its one of the biggest secrets in the wall that is full of enemies etc. In the Saturn version its just empty. Again if Im forgiving any developer for leaving things a bit unfinished, its Lobotomy.