Anon, entire episodes of chumash, tanach and bayis sheni aren’t mentioned until zman hagemara either. Many medrashim were written by amoraim, and the gemara itself has hundreds of stories about past events. The Mishnah doesn’t even mention the story of Chanukah.
So i really don’t understand your point about the mishnah not mentioning the talmidim of rebbe Akiva.
But your other point, of why we have a minhag for this tragedy and not others, i believe can be explained this way: seforim say that each of these talmidim were on the level of a tanna themselves. Think about what a loss it is when 24,000 tannaim, bekiim in shas, huge people, all are gone in 33 days. Imagine the national mourning, the state of shock and horror that klal yisroel was in during that time… Remember, our heros and leaders, all that we look to as important, were the talmidei chachamim.
This was a nation that was just exiled and stripped of its pride, the beis hamikdash, their homes, their parnosa, with many dead. All they had were the chachamim to give them life. And now they were dying everyday.
And they weren’t just dying everyday. They were dying during a joyous time. A time when we prepare for an annual kabolas hatorah. A time when our eyes are drawn heavenward, counting up and up and climbing the rungs of a ladder to Hashem.
And no one knew why! These were big tzadikim.
No one knew until chachamim later explained it.
No nahagu kovod ze lazeh! What does that mean? Were they nasty to each other? Of course not! The baalei musar say that it was very hard to see it. They would refer to each other by name, without saying Rav. They were too “heimish” and didn’t recognize that despite their friendship, they must honor the Torah inside them, which a chacham is not allowed to be mochel.
This answers your other question of went rebbe Akiva didn’t intervene. It was subtle, imperceivable, to all but Hashem.
And that’s why we mourn during sefirah.