First off, regardless of whether it was boxcutters/permissionable knives (and aren't boxcutters utilities knives and permissionable anyway?) fiberglass knives and other weapons exist (and have been sold) that would never been picked up by metal detectors.

Second, it wasn't that there wasn't much that they could do, it was that the SOP at the time was to go along with hijackers because they held the passengers and plane as a valuable object. Even though there had been previous attempts to use the plane itself as a weapon, such attacks had really not been successful and were therefore not considered.