The simple, necessarily out-of-universe answer is: Starfleet probably doesn't employ cetaceans. The "Cetacean Ops" bit in the TNG Technical Manual is a joke, part obvious nod to Star Trek IV: The Voyage Home, and part something humorous put there for the kinds of people who enjoy reading incredibly dense fictional technical manuals for fun. Cetacean Ops was never directly seen or referenced on screen during TNG's run or during the four movies. (See note below.) Lower Decks, ostensibly a comedy series, is just using some "deep cut" background material to make an in-joke to that part of the audience.
Episode writers diverged from the TNG Technical Manual plenty of times on-screen. For just one off-the-cuff example: according to the TNG Technical Manual, a Type-II phaser set to maximum is supposed to release enough energy to vaporize several thousand cubic meters of rock. (Apologies for the lack of citations and exact values. My Tech Manual is in a box and unavailable at the time of writing.) And yet, the on-screen usages of the Type-II at maximum -- complete with the FX shot showing all the bars fully lit, so there was no possible alternate interpretation -- did nothing more than vaporize a person. It certainly didn't vaporize the target, everyone else in the room, the room, the phaser itself... :)
If you accept that the TNG Technical Manual is canon, then you might as well start asking about the Enterprise-D's Porsche, the giant rubber duck, the second warp core, and why Starfleet decided it was important to write portions of the Gilligan's Island theme song in illegibly small letters on various bulkhead iconography. :)
(edited to add, because I suspect this will get asked)
Note re: Geordie's "have you seen the dolphins?" line in The Perfect Mate
While I hate to question the correctness of an answer to another question, the source linked in the answer to "Are there any other sentient species on Earth in the Star Trek universe?" for Cetacean Ops does not itself cite any sources. It includes a supposed Rick Sternbach quote without context, and that is all.
Geordie's line was not "Have you seen Cetacean Ops and the dolphins who pilot our ship?", it was "Have you seen the dolphins yet?" The existence of dolphins can be explained away by any number of necessarily hypothetical answers, because that is literally the only on-screen line about that in the episode dialogue.