I agree with Mark about the bottom shape being the biggest factor, however the materials and footpads also play a big part.
If you look at this guy's jibing video, it's amazing just how much a modern day board still flexes and this is on flat water!
...and that's a Wood Futura.
So if you imagine a stiffer, full carbon version of that Futura (or any brand), it is going to transfer even more jolt through to your legs.
Then add choppier waters...
Older boards (like you describe) like the Tiga, F2 Axxis/Ride, Mistral Flow/Screamer etc that were plastic skinned, had even more flex that really helped smooth out the ride, but because of their construction they were eventually prone to delaminating.
(Many of them also had a fair bit of Vee and were narrower, which also helped)
The other thing I've noticed more recently is how the soft marsh-mellow pads on boards like the RRD's and Tabou's also help aging knees deal with chop.