Yep, definetly for the knock sensor. Mine had one of the two on the male side of the clip broken as well. I didnt know it was for the knock sensor up until i tore down my engine harness to do my wire tuck and prep it for the aem install, eliminate all the unneeded wires, and change wires over for the map sensor and stuff like that.
I never had any negative effects. At the knock sensor you will only have one wire connecting. But on those you will have two wires. One wire on the female side right after that clip has a wire thats spliced in with the other with some type of diode or resistor or something under this nasty looking tar and tape. I would make sure its all wired up correctly when you put it back together for the knock sensor to work properly.
I have ran without a knock sensor plugged in many many times without any negative affect. Your car wont run on the knock map at all if it doesnt see any knock. lol. So if you want it to work properly then you need to wire it up just like it is. Dont eliminate any major part of the harness to do the repair.