Other mistake: In the anime scene, after the two men empty their magazines onto the back of Matsumoto, from under the bed, O-Ren shoots the leg of the guy wearing brown, then blasts his head. Then she fires a third shot that hits a brown leg, but the guy wearing blue falls instead. (00:41:55 - 00:42:40)
Other mistake: The Japanese phrase the chef says to The Bride when handing her the food is used after a meal, not before the meal.
Other mistake: At the end when The Bride cuts off the top of O-Ren's skull she somehow manages not to cut through the brain underneath.
Answer: From what I understand the reason for the lights being off is the same reason for why the previous scene was done in black and white; to decrease the amount of 'graphic violence' in the movie in an attempt to keep an 'R' rating. I would assume that they had him shut off the lights for that scene as just another method to accomplish that task.
I believe the original question was asking why was it done within the context of the film (i.e. why did the character shut off the lights) not why was it done in reality. My best guess is that the manager switched off the lights thinking the 88 had a better chance of killing the bride if she couldn't see. True, they couldn't see either but there were so many of them one could possibly have gotten to her.