The first scene of the 1984 movie does not exist in the books, even though they were depicted correctly. In fact, they didn't appear directly in the original Dune book at all, and they were only described in later books of the series (Both the 2021 and 1984 movies are adaptations of the first book, the 2021 one adapting the first 75% ish).
Two Guild Navigators are in the Emperor's party on Arrakis when he confronts the "upstart duke". They are not mutant freaks, they look like normal humans, but their eyes are so blue from spice use that they appear black.
The weird fish-baby in a tank is all David Lynch being David Lynch.
I looked up that part. Indeed there are two of the "guild agents, one tall and fat, one short and fat" as part of the entourage, and they are referred to in the text as Guildsmen. Paul asks them if they are both navigators and they reply with yes. And yeah they are revealed to have blue eyes, so I think this is correct. However, later books do describe the tanks in which the navigators live.
The dune wiki says that Herbert apparently liked how the navigators were depicted in the movie so he added their description to his last Dune book "Chapterhouse Dune". But even earlier books described the guild navigators as humanoid fish in a tank.
Apparently the explanation for these different forms is that there is a progression, where the guild navigators start out looking like humans, and eventually they look like the two in the Lynch movie.
IIRC spacing guild did try to keep their mutated navigators appearance secret from the general public, so having some normal-looking guild agents say "we're totally the navigators" does not really mean that they actually are navigators.
