>I'm assuming that therion uses the vertical difference between the highest station and the lowest station to generate the depth number without regard to LRUD data, is this correct?

Yes.

>And does anybody have a suggestion for how I can easily get the correct depth output onto my map?

You can add some tex code to a layout.   See http://therion.speleo.sk/wiki/doku.php?id=tex#overriding_data_supplied_by_therion_map_headers

Eg

  code tex-map
      \cavedepth{300\thinspace{}ft}  %forcing reported depth to 300 ft
  endcode

>I can see how this could be a significant issue if you had a cave with little vertical extent except for a high dome. You would have to shoot a shot to a station at the top of the dome to capture it's vertical extent in the legend data.

That would avoid the need to manually edit the depth each time you suspected a new survey might change the depth of the cave.  It would be my preferred method, even if it means creating an artificial shot to replicate the ‘up’ data.  It would need ‘flags duplicate’ to prevent it being added to the reported survey network length.

Bruce