That is, does the Overhead Press increase your chance of getting shoulder impingement syndrome if done repeatedly over a number of years, and does Pendlay rows (and bent over rows) increase the risk of developing herniated disks if done repeatedly over a number of years? Assume both exercises are done with good form.
Weight training injuries tend to occur due to muscular overuse. Having said that, there are some exercises that should be contraindicated for some people. In your example, the behind the neck press has certainly been indicated as a potential injury maker. I think the key to your question is the phrase
“...done repeatedly over a number of years”.
In my opinion, any exercise has the potential to cause injury even with proper form. Overuse Syndrome tends to occur after repeated trauma to muscular tissue. Overuse Syndrome becomes more of an issue as we age. Aging adults tend to require more recovery time. That sometimes does not happen between training sessions. Add repetitive motion to the mix for muscle tissue that has not fully recovered and you have the potential for an overuse injury.
I, for one, try to change my training on a four to six week cycle specifically to avoid repetitive motions. But, also to introduce new exercise movements that hopefully continue to assist in my training goals.
There is a lot of opinion on performing shoulder presses, a divided school of thought if you will. The only thing that I agree with about their statements on the shoulder press is the motion behind the neck. There may be some that can get away with that motion and not incur negative effects, but they're probably exceptionally flexible in their shoulder girdle; however, this is an edge case, not the norm.
The shoulder press, as Mark will demonstrate below, is the single best exercise for overall shoulder/trap developement.
Mark Rippetoe on the Shoulder Press
I don't agree with them about the barbell row exercise either. It is one thing if you have a pre-existing lower back injury relative to your lumbar vertebrae; otherwise, with proper form, this is one of the best exercises you can perform for your upper back musculature. If you want to perform a similar exercise and want to yield a similar effect, then you can perform variations of the lying row without stressing your lower back.
If you'd like to perform the barbell row as it was intended, check out th article and associated videos from Mehdi at StrongLifts.