With regard to these discount tickets - The price of discounted tickets for visitors from overseas has no bearing on real inflation (or nominal inflation) as far as residents of Japan are concerned, because the product isn't available to them. From the perspective of most overseas visitors, transport in Japan has deflated in real terms - as OSora pointed out. So if real prices are your criterion for evaluating the justification for price increases, JR is probably right to make the deal a little less sweet for visitors from overseas. No?

If you're making a general point about transportation costs in Japan - Yes. JR needs to look at its prices. But it's not true to say that transportation costs have not dropped. In fact, transportation costs have dropped due to (1) reductions in tolls for road travel (2) launch of real LCCs in air travel (3) growth of cheap bus routes.