I have been amateur EE and doing electronic repairs for fun for the past 2 decades.
When stuff fails due to external stimulus (like a lightning or connecting it the wrong way) things fail in a typical pattern starting from the power inlet, psu, and propagating into the device until it finds some things that can stop it. Voltage regulators, ripple capacitors, fuses, mosfet switches and so on are almost always dying first before any internal component.
Sometimes you get some stuff that is very fragile get hit somewhere in the middle of the circuit with everything around it intact. This is less likely than a typical path of destruction but happens.
But what you do not see is things that are quite tough get destroyed in a sea of a lot of fragile components that all somehow survive.
And that is because any device HAS to have a number of components on the power supply side that are put there with specific purpose of insulating the device from harmful outside signals as well as insulating outside from harmful signals from inside the device. It is not a choice of the designer, it is a regulatory requirement. You are required to do this to pass various certifications to be able to sell the device at all.
And so in all likelihood you (we) are right. The battery died on its own silently in the server while it was powered up. The battery does not do anything while the server is under power, it only takes over to power the internal RTC while there is no power supplied. Then you restart a number of servers and lo and behold, some of them have a boot warning possibly preventing the machine from rebooting complaining the battery is dead.
The servers were relatively new? It is possibly they were bought in bulk and all had the same faulty battery in them that had very short life span due to manufacturing issue. That isn't very rare.
This is way more likely than a lot of completely fine batteries get hit by a voltage spike in a middle of a fricking motherboard with nothing else damaged, in a large number of servers, the same way.