Does legion bonus empower invasion defence provided by council bases, lazuli pylons and soldier outposts?

yes, from my experiance it does.

are there anyways to destroy council bases and lazuli pylons?

yes. once you conquer the planet you hit the 'demolish' button. :P

unfortunately, no. thats why theyre 'better' than normal defenses. and thats why high levels pile their best planets with political favor buildings and npc drop structures. that way saboteurs and cluster missiles cant give the attacker an advantage.