In certain very restrictive conditions, yes, one or two engines might be shut down to conserve fuel in cruise flight. I expect that this would only be in an established cruise configuration, at altitude (allowing lots of room for a restart). I would extremely doubt that an antique former military airplane, particularly while carrying passengers, would ever have engines deliberately shut down in flight for reasons of economy.
It certainly serves the interest of preservation of these valuable historic assets to promote public participation, which might include experience flights. It's a fine line though, assuring an understanding of the possible increased risk in being a passenger on such a flight, as opposed to actually scaring people away. We don't want to scare people, but presenting the real facts of risk might do that. It is our moral responsibility to assure that potential passengers fairly know the risks. I am responsible for approving two now civilian certified former military airplanes to carry either passengers fully certified to do so, or crew only during restricted operations in a different role. Those crew members for restricted operations may still be new to flying, and are thus given a comprehensive briefing as to risks, and their duties as crew members - every person will have duties, which are real. No one has ever withdrawn following the briefings, which is nice, though as I conduct or witness at least some of these briefings, I assure that they meet the requirement of the flight authority I have endorsed.
I trust that the operator of the B-17 was providing reasonable briefings, and have no reason to think that they were lacking in any way. And, I'd believe that very eager passengers may see beyond "regular cautious understanding" for the opportunity to fly. But every now and then the worst outcome occurs, and reminds us to be thorough and realistic in our briefings of our passengers, to be as fair as possible. After more than twenty years of flying with me, and now following my being an a water flying accident, my wife chooses to no longer fly with me in the amphibian. I asked her what her reasoning was, and she replied: "having thought about it, now I'm not so sure that I could get my self out in a water crash if you could not help me.". A very fair, and considered answer, and I respect that from her. No pressure to her to fly with me, yes if she wants, no if not, she understands the risks, and I accept that.
Everything is a balance, sometimes it's a fine line. Understanding the risk is the first step.