The concept of storing knowledge in crystals, and subsequently learning abilities from them, isn't unique to FFXIV. This was actually quite common in Final Fantasy Tactics, for example, to the extent that it was even referenced in the game's preamble:
Sword in hand, a warrior clutches stone to breast
In sword etched he his fading memories
In stone, his tempered skill
By sword attested, by stone revealed
Their tale can now be told.
Crystals literally play a multi-faceted role in the Final Fantasy franchise. They could be the source of magic, a type of fuel and, in some cases, USB memory sticks not unlike Allagan tomestones. 
And because of their use as "shortcuts" to learning a job in FFXIV, I've always felt that the "jobs" we currently know are really no more than pale imitations of what they had been in the past.
Consider this: The way we use "jobs" in the Seventh Astral Era is through a mix of class kills and a handful of job skills acquired from the stones. I doubt that an Allagan summoner of yore mixes modern arcanima with his or her magic, for example.
It also means that there may have been a lot more to the original jobs that are forever lost to time, that we now try to emulate through modern skills that are functionally equivalent to those of the job.
And I suspect that the dark knight will be explained as a "job" that exists only in modern Eorzea. It has no historical precedent, making it therefore unnecessary to "restore" it through the use of a soul crystal. From a lore perspective, it would also mean that learning the job would entail starting from scratch, from the very basics of harnessing one's rage and dark energies, to perform the role.
As for why we haven't actually "seen" a dark knight, it's probably because it's more exclusive than the typical war and magic disciplines, which have their respective guilds all across Eorzea.
So, I suspect the dark knight will be FFXIV's equivalent of a Dungeons & Dragons (3rd edition) prestige class.