A raiding guild for 40 players is typically composed of no less than 60-70 regular players to deal with precisely this problem. Top guilds will often have enough players to fill three or more raid groups in order to have enough prepared players for the "main raid."
That's a bit of an exaggeration. A lot of guilds can barely fill their raid roster. They manage by strongly pressuring all raiders to show up every day on time, and to give advance notice if they need to be out.
Speaking personally, until very recently my regular raiding guild only had about 26 or so raiders who could show up every night (and another 3 or 4 who could show up for 1 or 2 of the nights). And yet we still managed to clear 8/8H.
And there's a reason they got rid of them. Spending two hours of your life waiting for people to log, relog, get add-ons, read and repeat boss fight documentation just to spend another 6 wiping with ninja loggers wasn't very fun.
Those of us that got heavily into EverQuest "back in the day" recall raids that involved these kinds of numbers (50+) and took place over 8-10 hour periods. It was possible to achieve with sufficient planning, a dedicated guild, and a compulsion overwhelmed the need to sleep, eat, or view the sun.
I'm not proud of those days, but it did help me realize the key to managing any large group of people: make it feel like work, make everyone believe that it is a job and not a leisure activity so that you feel obligated to stay despite a complete lack of anything resembling fun.
So, yeah, I can imagine this actually happening. If you could do it with EverQuest, you can probably manage to achieve it with Minecraft.
