Many people experience more aches and pains as they age. However, it's not a guarantee. Knees don't just 'go bad' most of the time and pain doesn't automatically mean there is damage either.
Sure there are some disorders like osgood schlatters and osteoarthritis and so on and so forth, but even for these staying active usually helps dramatically with the symptoms. Exercise is still one of the most common recommendations for pretty much any health issue, including musculoskeletal.
It's possible the knee pain is because you just started running again after some time off. It's also possible the knee pain is because your routine sounds overly repetitive (i.e. overuse injury). It's possible a shoe change or a sock change or a route change is the issue too.
The internet sadly cannot help you here.
You should go and see a physical therapist to address the knee(s). Figure out what the problem is, devise a plan to fix it with your therapist and return to sport.
Contrary to the internet belief that squats cure all, movement variability is important. When you get back into a routine, do keep in mind that you likely need some variety beyond squats (especially if running is your true passion here) unless you want to compete in powerlifting. If you're not a competitive powerlifter, then lunge, deadlift, single leg hinge, step up, side lunge, single leg squat, etc...etc... make sure you have some variety in your routine. Some variety is important, but I wouldn't mix things up every time you train either (you need a few weeks to adapt to any given routine).
I'd discuss this further either with your therapist, or a strength and conditioning coach of some sort.