why is the pc-engine one more expensive
I don't know, but I can speculate. I think Ninja Spirt NA vs JP is comparable to Keith Courage vs. Wataru:
Wataru is, surprisingly, more expensive than Keith Courage. KC is common in North America (it was a pack-in game, large quantity manufactured, demand for it is relatively low).
Wataru, I suppose, may not have been produced in as large numbers as KC. Also, I'm not sure if Wataru's tie-in to a television show would increase or decrease its desirability these days...
Ninja Spirit, while not an official pack-in, seems to have been produced in large amounts (it was considered as a pack-in for the DUO, IIRC. Whether this is because it is a good game or because NEC/TTi was stuck with a huge backstock and wanted to get rid of them is another story).