While most nerfs are announced that they will happen before they actually happen, a ninja nerf is simply done, leaving the players to discover, usually being completely screwed over at the same time due to being surprised.
Player B: Ok, let's go. Those shifter tanks get like 2000 hp, so we should be fine.
*Player A and B get to the Boss*
Player A: omfg Wtf!? I've only got 800 hp!? *dies*
Player B: Oh Fuck... *dies*
Player A: Well wtf... I had 2000 hp yesterday... I didn't see anything about a nerf on the forums, did you?
Player B: Nope. Must have been a ninja nerf.