Landing too heavily when you run cannot be good for some parts of the body particularly long term. Being flatfooted or running on tired legs could result in heavy landing also.
I think you will find solutions very subjective, what suits one runner may not suit another. However, strong legs that can see you comfortably through your chosen race distances are desirable. You could try running shorter distances with a focus only on softer landing. Doing that often enough may result in some improvement.
Sometimes when I find the going tough I will say to myself "soft - lee, soft - lee" as each foot hits the ground to focus on landing softly. Another mind game is to imagine you are running barefoot on broken glass to encourage both a quicker pace and softer landing. Shoes alone, I don't think are the solution.
I am guessing that you have increased your mileage from 20mpw.
If I am correct, even now a sensible 'long run' would be 9 or 10 miles. If you are attempting 16 miles with "three pretty big hills" at the start no wonder you are suffering.
How fast were you running your 20mpw? Long runs are usually long slow runs (LSR) so why complain that you are down to 11 minute miles? If your 20mpw were mainly 8 minute miles 11 minute miles for 16 miles in one mighty effort seems fine! The main purpose of long runs is usually to train the body to burn carbohydrate/fat efficiently, Speed is usually only a secondary consideration.