They do, and yes. Generally mixing and matching batteries of different ages is bad. Police and gov units buy batteries at the same time as the fleet or replace them all in a batch. This way they all should be fairly similar on age/number of miles.
Generally, if you have say a 2020 battery and a 2016 battery in a bike, you'd expect to see increased wear on the 2020 battery, decreased performance, issues at lower SOC and SOC fluctuations. Just due to things like different battery chemistries and wear levels. It's a bit better recently since the chemistry hasn't changed since 2016MY. but the wear issue is huge,
About a year ago we had a rash of powertank/monolith bikes stranding people because the newer power tank and older monolith discharge at different rates on a ride, and the voltages were too far apart to safely close the contactors once they tried to go again. Software fixes were applied, but the issue remained. Most of those bikes got both their batteries replaced, and Zero started mandating no power tanks for bikes past a certain age.
Generally we advise people to buy 2 modular FX batteries if they want that, and a powertank soon after the monolith for the same reasons. Zero seems to be moving away from the modular FX, I think they stopped selling them in the EU.
I feel bad for the people who's batteries give out outside of warranty. They're expensive, replacing them isn't always cost effective. I'm sure Zero would love to allow us to do cheaper cell box repairs, or charge for refurbishment, it just doesn't seem to be possible with today's battery tech.