There is a huge difference between unitary states and federations. American states have legislatures, constitutions, and nearly unlimited rights to raise taxes. Prefectures in Japan are much closer to counties in the U.S. US states are much close to independent countries than to administrative subdivisions in unitary countries.
> Looks like if the U.S. had the national representation (population per seat) of Japan we would have over 1000 reps, South Korea almost 2000.
On the other hand it's about on par with the EU parliament. What would the advantages of significantly increasing the number of representatives be? Most individual matters should be addressed to state officials anyway.