If you're not blending 100 at a time then you don't need them lol. IDK how much resources are used by disconnected clips into layers? I would assume that if a layer is disconnected it still has to be processed as it's apart of the overall mixer. It may just see no input and then move on, but that layer still has to be asked what's going on and that's processing.
Columns DO have remove before and after, so it sounds like columns are exactly what you are after!
Maybe change your comp mode to connect clips to the "Selected Layer" and then just select an open layer and click a clip. When you're done, just remove all after or before and you're ready for the next one.
You could add like 2-3 layer extra on top of the max amount you plan on blending just to have a few extra slots open to cue up clips, but 100 layers...... ppppffff... that's wild!