I don't know about anyone affiliated with the show, but Barry Freiman (d. 2012) has discussed this. He was a freelance writer who, among other things, was a Superman guru, reporting and contributing to many of the Superman fan sites, e.g. Superman Homepage and Superboy Homepage.
He wrote an article on the Superman Homepage where he stated:
Almost everyone knows that comedian Jerry Seinfeld is a big Superman
fan. But an urban legend has sprung up that Jerry snuck a reference to
the Man of Steel in every episode of NBC's Must-See comedy juggernaut,
"Seinfeld", which aired from 1989 to 1998. Not true.
Thanks to my TIVO, I've taken a ride around the syndication wheel of
"Seinfeld" repeats on TBS over the past few months, screening the
episodes for Superman references. As it turns out...[despite many appearances] it's still far from something super snuck into
every episode.
On the article, he does include a link to every episode which contains a Superman reference.
Now, whilst this isn't the completely conclusive answer you were after, given Freiman's prominence in the Superman world, I think his opinion on the subject does carry substantial weight and thus I would say: no, not every Seinfeld episode contains Superman references.
Edit:
Okay, some definitive proof. Interview with Jerry Seinfeld, in July 2014, conducted on Reddit:
[Question] There is a rumor that there is a Superman reference in every episode
of Seinfeld. Can you confirm or deny this and who's idea was it to put
the references in the show?
[Jerry] I can deny it categorically. You can't count seeing the little
Superman model on the bookshelf as a Superman reference. I would say
there are maybe 10 Superman references out of a whole 180 or so
episodes, so that's a long way from all of them.
Peter Mehlman, a writer for Seinfeld, also comments:
Contrary to rumor, it was never planned to make the Man of Steel a
recurring theme, and the writing staff, on which I worked for six
seasons, never got an edict dictating regular mentions of him.
Whilst this certainly isn't as categorical a denial as Jerry Seinfeld provides, it does show that the writers were certainly not instructed or primarily interested in dropping these references - rather it was just an entertaining side project that happened occasionally, with the fans taking it to whole new levels (e.g. if Jerry wears red and blue, fans of the theory consider that a link).
