Oleg I think you are right.
I did some observation in a simultaneous game, where you can login into an empire without turning it to human control. And indeed there were some empires thar scrapped the same type of non obsolete space yard base while building a new one of the same type. Without the AI bonus the resource spending exceeded the income which probably caused the scrapping. However the game had a high AI bonus (= 5x production) which was shown correctely in the empire status window.
My conclusion is that the AI indeed still does not take the bonus into consideration when he has to decide if scrapping is needed.
