JJ2's original resolution was 320x200, not 320x240, but neither of them was ever removed from the game. You can change the resolution in the Options > Video menu from the root menu; from the Video dropdown menu in windowed mode; or by pressing Ctrl+F1 (for x200) or Ctrl+F2 (for x240) while in a level.

If a specific resolution does not appear in the list, you may be playing in fullscreen, and your GPU may not support that resolution. You will need to add it your GPU's listed of supported resolutions.