You don't have to ask yourself anything. It is Clear what bonus objectives are. It is a completely different type to side Quests we have now.
Best example would be Harrison Jones Questline in Uldum, after you land from the Box you get a quest off the ground to make a Tablet by collecting fragment parts.
Whilst doing this part of the quest there are Hyenas around everywhere, when you kill one you get a Automatic Bonus Quest pop up on your screen that says "blah blah Hyenas are Bad, blah blah Kill x10 hyenas" with no real story other than "Hyenas are bad blah blah". You still do your Tablet collection but you are also killing the mobs in an area, to actually encourage the players to kill things instead of just trying to dodge Mobs while they collect pieces.
All Blizzard are doing is when you kill the "Hyena" now, instead of getting a pop up screen with some half-assed story about "Hyenas" being bad, you will just get a Number counter to the side that will say "Hyenas" Slain: #.
You will still be Following Quest lines, You will just have more bonuses on the Creatures that surround the areas you are questing in.
Embrace it, since it means less Quest clutter and you will actually probably get a lot more bonus objectives.