The domestic flight experience on Japanese airlines is very no-frills indeed. You could be on a 3.5 hour flight to Ishigaki with no food and (if an older plane) no entertainment whatsoever. It can be surprising to people from other countries.
That said, JL does serve a few drink options in economy, like coffee, apple juice, and consomme soup.
And I totally agree with you about the frustrating lack of decent food available for purchase at the airports. With most passengers getting no food inflight, you would think that there would be a huge market for quality bento meals in the terminals, but nope.
ANA differs from JAL in that ANA offers a premium cabin on almost all domestic flights, so with ANA there is at least an option to get meals inflight on almost all routes. ANA's premium cabin service is not as nice as JAL F, but it is MUCH more widely available.