> But is it really sensible to plow money into (say) the Hokkaido Shinkansen, on Japan's most rapidly depopulating island and not remotely competitive with flights in travel time or price
Yes. Sapporo has a population of 2 million; many of the rest of people going to Tokyo from the rest of Hokkaido will travel via Sapporo Station regardless (I know I always did - multi hour bus or train ride to Sapporo station, then another train to New Chitose, then flight to wherever). The flight route is incredibly busy (from one source, "The route between Sapporo and Haneda was the busiest in Japan and the second busiest domestic route in the world in 2019"). Work trips will likely pay for train rather than flights, while tourists mostly use JR passes and will choose the train as it's "free". Carbon intensity of electric shinkansen is dramatically lower than the excessive number of flights going between Tokyo and Sapporo. It'll be 4.5 hours city centre to city centre, which is easily competitive with flights unless you happen to live in Chitose and be heading to Chiba or Yokohama.
> the Tsuruga extension to a city of 60,000
This is disingenuous: the extension is an intermediate phase connecting Nagano (low population but huge winter tourism) with Kyoto/Osaka (idk, 25 million? and massive tourist destination).
> the greenfield Noto Airport that can't support two flights a day without heavy subsidies
Per the wiki article [1], it seems like the airport has been reasonably even (ANA subsidizing airport sometimes, prefectural govt subsidizing at other times). A lot of local governments in other areas (including north america) also subsidize their airports to ensure accessibility for residents.
> and a million minor construction projects damming up rivers and coating the coast in concrete tetrapods
They aren't all tetrapodal! Their work in this area is pretty singlemindedly focused on reducing flood/tsunami risk, with 0 concern for environmental effects.
[1] https://en.wikipedia.org/wiki/Noto_Airport