I believe that the 0 health buildings does go against logic but for some fluke it might actually be gameplay enhancing. I for one believe so and it has been engrained into my gameplay style to manually search-out 0 hp buildings , even scout for them and send in opportunistic attacks just to kill 0 hp buildings. I think its fun and a test of your awareness in-game. However I do see it been a problem if your not the sort of player who microes his battles...
Oh, i micro them, but its also the same for the AI, they simply CAN´T destroy them.
You can build indefinitly new gauss cannons in your line while the AI attacks them, since they rarely target the builder and wont target the non-built ones.
I don´t know if they´d attack these buildings after they take a planet (never lost one against the AI

) but probably not. And as it takes up logistical and tactical slots to build they won´t be able to utilize the planet properly.
On that note:
Ihad a situation, where i had taken a planet and the asteorids for res were not occupied, but there was a huge asset of other buildings in the gravwell.
Since the planet resets i had used 12/6 logistical slots (even though i had no own buildings)
And i couldn´t build any extractors, even though they take 0 slots (the game said there were no free logistical slots)
I think this should be fixed aswell!