We created the "Hide read labels" and "Hide Labels from Subjects" labs to help people manage their ever-growing lists of labels. Given the popularity and usefulness of these labs, we've decided to graduate them into fully-fledged features. We've also made a few improvements to how they work. First, instead of simply hiding all labels from subject lines, you can now choose which labels to show or hide. We also spiffed up and organized the Labels tab in Settings as well as the dropdown menus for each label in the label list.
If you had enabled either Labs feature, your settings should automatically be carried over. If there was a glitch in the matrix, or if you want to change the visibility for a bunch of labels quickly, you can adjust them en masse by going to the Labels tab in Settings.