What is the fastest possible way for you to stop?
For me, it's pulling hard on the front brake, with my rear end well behind the seat. Ideally my rear wheel will be a couple inches off the ground the whole time. Actually achieving this is virtually impossible, but it should be the goal.
The braking technique you should use is a "light" version of whatever can haul you to a stop the quickest. Every time you come to a stoplight, or are reducing speed on a descent, use your front brake and push your rear end a little further back (or whatever technique works best for you). You don't have to brake hard. Just connect those motions in your mind by doing it every time.
The benefit of this is that when you suddenly have to do an emergency stop, you will instinctively do the best possible thing.
So to answer your question, yes, you should shift your weight back when you brake (along with bracing your arms, of course). Because if you don't, you will fail to do so in an emergency stop, when it really matters.
I completely disagree with Jobst Brandt's theory. Bracing your arms against hard braking is of course necessary, but it's completely instinctive, and therefore not a problem. What's not instinctive is 1. using your front brake, and 2. shifting your weight back. Your goal should be to make those instinctive too.
On top of this, you could further hedge against going OTB by practice stoppies (lifting the rear wheel under hard braking). If you do this, you will be much more in control during emergency stops.