Onslaught might not be suitable for immediate use anyway at this point. Because the way that Onslaught was dealt with, needed some extra characters which currently do not exist in the X-Men 97 cartoon; primarily Franklin Richards (Son of Mr Fantastic) and Nate Grey (Alternate Universe Cable). And given Nate Grey (X-Man - the primary source that taught Onslaught unwittingly how to form Psychic energy into reality) is heavily tied to Apocalypse, the writers likely went with the Apocalypse route first so they can be brought in later to bring in Onslaught and the other Marvel characters. Possibly by giving some Age of Apocalypse stuff too.
Especially since they can write about the idea of AU versions of characters and whether they are the same or not; Nathan Summers vs Nate Grey. Which is often written about in the comics when both are in the same story together.
Nightcrawler becoming wide eyed on seeing En Sabah Nur, and everyone who fought Apocalypse before on the episode with (the Celestial) "Ship" and "Ship" expounding on Apolcaypses past would suggest that they know they are face to face with Apocalypse pre-celestial tech.
As for Cable, I think it was intended for Cable to be fodder for now. Because Cable was at one point, going toe to toe with Silver Surfer (Herald of Galactus). So letting them be at full power will make the full team working together at the end kinda moot. And of course, if Nate Grey is brought in, then you can have the difference of power use between them as a story point to differentiate them. One is about using power efficiently to great effect; the other is about having so much power they can afford to go all out all the time to extraordinary effect (in essence, they can't of course due to "reasons").
