Have two people know all the passwords. Let each of them encrypt this list of passwords with a password only they individually know. Sync passwords each time someone changes something.
If I have that many servers then I can assume I have a large budget for security, right?
I would make a password entering automation system. Ensure that that system is dead-simple and secured to death. It must run no other services, firewalled to death even from the intranet, physically secured in a cage, and must be off most of the time. It is only to be turned on when booting a system, and turning it on not only requires a password but also physically walking to the cage, opening it with a physical key, and pressing the "on" button. All target servers must be configured in such a way that they can obtain network access before mounting the encrypted part.
But I'm not a security expert. Maybe I've overlooked something.
It's harder to set up. But when the password entering automation system exists, you just grab the key, go to that system, unlock & boot it, then tell it to enter the passwords for your 1000 servers.
I'm not sure you can assume that if you're, say, Instagram (pre-big-round/acquisition). You may well have several hundred, even thousands, of AWS instances with a staff in single digits.