I'd say it depends on the game.
Middle school, we have a rule to never 45. Middle school is developmental and as a coach you can totally control a game. i want as many reps as I can get and I can always find players to run the ball that will keep us from scoring quickly, or scoring at all. At our first game this year the other team's primary RB was a no-show. They had several 6th graders against my 8th graders. The game could have been over at half, but I put in my whole bench in the second quarter and told them not to rush (the other team was having a hard time with snaps) and to wait for them at the line and do your best to tackle once they got to you. The other team started throwing and my boys came over at the end of the quarter and asked what are we supposed to do now? I said now we work on pass coverage. Let them throw. At half, I went to the other coaches and asked what they wanted me to do. I told them I could keep it going like this or I could end it if they wanted to go home. They said let's keep it going. We played the whole game much to the chagrin of the officials. We still won, the other boys had a good time throwing the ball around, and I had two kids who never run the ball, much less score a TD, score a TD. I believe there is hardly any situation to 45 a team in middle school. Cheap shots are about the only reason.
In high school, if it is a non-district game, I put in whatever I have on the bench to keep the game going to get my young boys some reps. They have to get reps in some game and this is a perfect opportunity.
During district play, it's business and I can see the wisdom in getting done with it. Injuries, cheap shots, huge turns of events, who knows what will happen. Just get the game over and on to the next one with your full team in tact. One key injury in 6-man can totally change your season.