This is not true. In 2e, ninja was it's own class, belonging to the rogue group. In the same way a paladin was it's own class, but belonged to the warrior group. And why? Because of the varied specialties of the ninja (the warriors, the spies, the magic users, etc--which were what the actual kits were within the ninja class). Which is the best justification for it having it's own class in 5e because 5e's subclass system is made for it perfectly. I.e., a core ninja class of core features, then a subclass for the front line ninja warriors, a subclass for the spies and espionage, and a subclass for the arcane magic users.
Certainly one of the better arguments for dedicated classes for old OA classes (at least for the ninja). Even in 1e, the ninja was a weird kind of multiclass character, where the other class was their 'cover' class. 2e's Ninja's Handbook cleaned that up quite well with the various kits and the 'shinobi' approach to other classes being members of a ninja clan.
Still, I do like the idea of not adding more dedicated classes but expanding on adding subclasses. It could be just as easy to add a ninja subclass to the various base classes to reflect the specialized training a ninja might receive within their clan. It also fits quite well the mystique of the ninja being "everyone and no one" (if you subscribe to that particular aspect of what a ninja is/was). This, I think/feel, would allow the ninja to hearken back to both 1e and 2e in feel and approach, while maintaining 5e's more approachable/less bloat overall aesthetic.
So you could have something like this:
Fighter subclass (Shadow Warrior): The front line ninja warriors
Rogue subclass (Stealer-In and/or Intruder): The espionage/spy specialists
Wizard/Sorcerer subclass (Spirit Warrior): The 'ninja magic' practitioners
Bard subclass (Consort): The open infiltration specialists
Ranger subclass (Pathfinder): Terrain intelligence...sort of goes out and scouts the terrain for future operations in that area
This latter approach does obviously "scatter" the ninja concept (and would be best if done in a single book for the sake of ease of use), but it does fit the various previous editions approach and really drives home that ninja could be anyone...you just never know.