Quick question as to whether adjacency bonuses to Planetary Defense improvements (i.e. elerium defense shield, planetary defense dome) are supposed to be included in Planetary Defense Percentage or if it is a bug if they are not being included. Checking my current game (1.5) none of the adjacency bonuses seem to be included in the planetary defense percentage on the world that they exist on or any other world.
The Planetary Defense System's and Planetary Defense Dome's level bonuses work as far as I can tell. You might have overlooked the fact that the level bonus is not counted separately from the improvement's basic bonus in the tool tip; a level 2 Planetary Defense Dome will show up as providing a 60% defense bonus in the tool tip rather than a 50% planetary defense bonus with a separate 10% bonus for its levels.
The Elerium Defense Shield's level bonus does not work, which in my view is a good thing since at present it's defined to be an empire-wide bonus and that, particularly in combination with the other obtainable bonuses to planetary defense, would make it fairly trivially easy to render your entire empire immune to invasion.