Do you know if running on the beach (or sand) is better on the joints? It seems like it would be better on the joints, plus it seems harder (better exercise). And hey, you're on a beach.
Running in sand usually causes quite a bit more load on your achilles tendons. The pitch also causes one foot to underpronate and one to overpronate which is also usually a bad idea.
Most of peoples' issues relate to bad form, muscle imbalances, etc. Although I will grant if your form is terrible you are probably going to put weird stresses on your knees, etc. I blame our incredibly sedentary lifestyle. I sit probably 60+ hours a week (job, commute, home, etc.) and run only about 4 hours a week (~30 miles). I have been racing and running for close to 25 years and most of my current issues came from very hard training in the past and not taking time off when I got injured. When I just run 4 to 6 miles "easy" I am basically injury free as long as I supplement with a few other exercises such as single leg partial squats and monster walks with a rubber band. These are mostly only required because of my sedentary job and not the running though.
I have no problems with my shins and knees since I'm running mostly mid to slightly forefoot strikes. The forefoot absorbs the shock rather than pounding the knee and hip with a direct impact. When I run with shoes on pavement, I get some knee and hip issues, especially if I don't pay attention to my foot strikes with respect to changing pavement.
My anecdotal data says that if you don't live near a beach, dial back a bit while on vacation at a beach. I can't say why, but too much leaves me with connective tissue soreness. Probably just not being used to it, because I otherwise typically run a lot.