Fix a few issues with the new bookmarks handling code

I noticed a few issues with the way bookmarks are handled since f96357d. For instance, clearing the bookmarks file manually without resetting the sidebar-bookmark-breakpoint value as well, would cause newly added bookmarks to remain hidden despite the "Bookmarks" section being shown in the sidebar. Moreover, this PR avoids a segmentation fault caused by a missing NULL check in the DND code.
We need to update the gsettings key when doing a correction like this (either during the first run - when the key is set to -1, or in other situations where the breakpoint becomes longer than the list length.