In your user settings you can define how many note's levels you would like to see.

• Note depth
  defines for how many levels you want to see the title of notes. You should normally put that to a large number like 66 because you want to see all notes.
• Note text threshold
  defines up to which level you want to see the note's text. This should normally be a smaller number (like 6) so that you don't have to scroll too much if two people got into a length 'discussion'.

-- Hofmator

Also, if you just click on the parent of one of the undisplayed messages, the undisplayed messages will no longer be below your chosen depth. So you can always get to the undisplayed messages without making a big fuss in your settings.

-- Frag.