Some dialogue in VOY: Dragon's Teeth suggests that as of the 15th Century AD, the Borg had only assimilated a few dozen systems. Seven mentions that the Borg's memories of this period are extremely fragmented.
GEDRIN: You're Borg.
SEVEN: How do you know that?
GEDRIN: Don't you recognise my people? The Vaadwaur?
SEVEN: The Collective's memory from nine hundred years ago is fragmentary.
GEDRIN: I've had many encounters with your kind.
Why are the Borg unable to remember that far back very well?
The early days of the Collective are shrouded in mystery and largely contradictory. What we do know is that at some point in the Collective's life, a species was discovered that had a special ability to "bring order" to the chaotic thoughts of the various lifeforms that made up the Borg hive-mind.
Given that the species designation of the Borg Queen is relatively low (Species 125), it's certainly plausible that during the early chaotic portion of the Borg's existence, records were patchy and not shared across the Collective in an orderly fashion until her/their assimilation took place.
BORG QUEEN: You imply disparity where none exists. I am the collective.
DATA: Perhaps I should rephrase the question. I wish to understand the organisational relationship. Are you their leader?
BORG QUEEN: I bring order to chaos.
Maybe they just don't want to remember the Vaadwaur. I posit that the Borg, being a particularly unsentimental folk, intentionally purge some memory files as part of bringing order to chaos.
The Borg are interested in things that are biologically or technologically "distinctive." The Vaadwaur were pretty much destroyed by the Turei 900 years ago. At the time, the Borg only controlled "a few systems." The Turei then took over the "Underspace" corridors.
Cut to today: We know the Borg didn't take over the Vaadwaur homeworld. If the Borg encountered any Vaadwaur or Turei in the last 900 years they would know about the subspace corridors. Yet, the Turei confidently lay claim to the entire network and don't seem worried about the Borg (though this could be sheer bravado). In other words: the Borg are not interested in the Underspace or the Turei and certainly not interested in the Vaadwaur.
If you want to bringing order to chaos, it probably helps not to spend time thinking about the Vaadwaur, just like you and I don't spend a lot of time thinking about Milli Vanilli. In fact, when a Milli Vanilli earworm pops up it's really quite distracting. If I could flip a switch and erase my memories of Milli Vanilli, I probably would. And I think the Borg Queen agrees with me. Girl, you know it's true.
If I remember correctly, Seven stated that only relevant memories were retained by the collective, not everything. As time goes by, things that may have appeared relevant once get overwritten by something more relevant. A simple example would be anyone's childhood memories. They are typically fragmented and become even more so as people get older. So, after 900 years, most information would no longer be relevant or of much value. Especially since Vaadwaur got almost completely wiped out during their battle with Turei, and the survivors were stuck in the hibernation pods! What was the meaning of word vaadwaur in the old Tongue, according to Neelix? Foolish with a notion of bad behavior (some tale about the boy who lost his head). So, if I were Borg, I think I would not remember them either! Not my most favorite episode... :)
One reason is because so many Borg died. If you kill enough Borg theoretically you could give the Borg fragmentary memory.
