Many, many times. Many breaks are taken for lots of different purposes: bathroom breaks for jurors, cigarette breaks for jurors, the judge is hungry, taking a break to hear an objection in chambers, taking a break to discuss settlement prospects, etc. Court is not 9 through 4:30 nose to the grindstone. It's a little more laid back than that.
That's probably why the judge in this case is allowing the prayer breaks. He or she just doesn't give a shit. After all, what are two more breaks per day (which would probably be scheduled to coincide with other breaks)?
And, I actually commend the judge for doing this. Aside from these maniac racists like you drawing attention to this issue, allowing prayer breaks actually minimizes distracting protests and media coverage. It keeps the issue to these Defendants' alleged crimes. And it avoids any lawsuits brought by the Muslims concerning their right to take prayer breaks. And it prevents any claims as to the integrity of the trial (e.g., that the judge was biased against Muslims).
But no, let's let racism prevail over logic! That's the American way!