Do stained glass windows fade over time?

The glass itself doesn't fade. It's the lead that changes tone over time. If your leaded windows are getting a lot of direct sun every day, they're going to take on more heat than a window that's more sheltered. That's just part of the natural aging process. There's not a lot you can do to prevent it beyond having an awning or porch that blocks some of the direct sunlight. But honestly, there are windows across Toronto that have been exposed to natural sunlight for over a hundred years and they're still standing. This is a long game. Unless you're planning to live over a hundred years, it's probably not something you need to worry about.