This issue already has a bug logged for it: MISSING TOGGLE BOOKMARK MENU ITEM IN PLSQL EDITOR. Currently its Fix By is set to 4.0. As this functionality comes with the JDev IDE infrastructure, it is not clear to me whether it just did not get hooked up properly when we re-based on JDev 12c or perhaps there is some other complication. You will note the Bookmark preferences node for the Code Editor no longer appears in 4.0, and the same is true of that feature's shortcut keys in the Shortcut preferences.
Some common complaints with the 3.2 and earlier releases was that Bookmarks did not work at all for the Worksheet and did not persist across sessions for the PL/SQL Code Editor. Once the bug is fixed, let's hope there are improvements in those other areas too.
SQL Developer Team