I think it's pretty much plain physics... when you are decelerating your weight transfer of the bike goes from - let's assume 50/50 front/rear - to 60/40 front/ rear.. etc... so more pressure and weight is on the front suspension.
At that point, there are many factors that can contribute to a head shake... weak fork springs, rear suspension, worn front - and yes, worn rear - tires, road surface, tire pressure and even the wind.
Ever see sport bike races when the bikes power our of a corner on to a straight? Their front wheel will many times wobble due to the weight transfer from front-to-rear... same physics will apply to acceleration as well as decel.. However, most of us don't have the horsepower, or nerve, to see the effect coming out of a corner.
I'm not saying anyone should ignore these things when they happen because you could have a valid issue.. just saying there are physics involved and other factors that may be normal.