Yes, it will. "All Enemy Defensive Tower" applies to many things (e.g., air defense, towers, mortar, redoubt, ... everything that shoots, basically), so this logic applies to all of them.
The question is if I have -50% All enemy towers Hitpoints and -15% enemy missile silo Hitpoints, is that -65% Hitpoints for the missile silo to 35% Hitpoints or -15% to 85% and then -50% of the 85% to 42.5% of Hitpoints.
I believe all bonuses operate this way: There is a base number. Then all of the bonus percentages get added together (so 50% + 15% = 75%) and after all bonuses are added together, they get applied onto the base number. I think they've confirmed this a number of times