Does cycling make one's knees stronger? I'm wondering if riding hard strengthens the knee or causes degradation?

I exercise regularly and am in solid physical condition.  When strength training off of the bike, I do a lot of leg work including heavy squats, deadlifts, lunges, etc.  I've been doing this seriously for 5 years or so alongside riding, mostly road, and it's done nothing but help when I get in the saddle.

So, when I get on the bike and ride hard, which is usually 4-5 days a week in season, I have leg soreness (obviously).  However, I get sore in the knee - not pain per se - just soreness.  The soreness is mostly felt in the structures that hold the knee together, i.e. ACL, MCL, LCL.

When I strength train I don't get sore like this - the soreness is all in the muscles, i.e. quads, glutes, hamstrings, as opposed to the ligaments.  In fact, I've never done anything besides cycling which induces this type of soreness.  That said, is this good in the long run?  Am I strengthening my knees or slowly working toward future knee problems?
The key point in your question is I get on the bike and ride hard.

There's nothing wrong with riding hard, but it sounds like you're riding too hard for your knees to be happy.

Since you like doing weights, I suspect that you like to push the pedals hard, and this is causing the problem.

Bike fit issues can cause knee soreness, but they also tend to have other symptoms also, such as back soreness or neck pain.

The solution is to train yourself to ride with higher cadence, ie to spin the pedals faster. Aim to get into the 90-100 rpm range, or even higher.

There are many questions here tagged cadence, the most useful for you may be What is the optimal cadence? and will increasing cadence ability hurt my climbing strength?.