Check all of the tooltips on your spells and skills. They are divided into 3 groups: Weaponskills , Spells, and Abilities.
Pacification will block weaponskills (things that cost TP to use)
Silence will block spells (things that cost MP )
Abilities cost neither TP nor MP, and will be unaffected by those debuffs. So things such as Fester, Lustrate, Brutal Swing, Bloodletter etc. will always be available barring all-encompassing debuffs such as Stone, Stun and Sleep.
Almost all abilities used by enemies are exactly that, abilities. Unless SE decides they want us to stop a specific ability as part of a combat mechanic, using Shield Swipe for the Pacification is primarily a PvP tool, while the TP savings are certainly worth noting in longer PvE encounters.