The reason you see them with low mileage is because they're Miatas. Usually a second car, and a very high number are precious and only go out for special occasions. The 1999 isn't unusual one way or the other in this regard.
Pretty much all the cars that were liable to have the thrust bearing problem (described as a machining problem at the factory, but there was a bearing size change midstream and I suspect some engines got the wrong bearing installed) have had it. If the car hasn't had the problem by 20k, it's not going to.
The 1999-00 head (which is also the rarest) is viewed as the best Miata head, but I think the VVT 2001-05 one is better if you have engine management that can take care of it. Those who say VVT doesn't do anything have never tried.
Dad didn't buy #338 new. He picked it up in 1999 or so after it had spent a year bouncing around various car lots. An afternoon of polishing added about a grand to the value of the car. A friend of mine has #26, a pre-production model that was supposed to be crushed but escaped. Lots of really interesting little detail differences on that one.
