Firstly, that's not what it states:
Lord Vitiate orchestrated the sorcery and the planet Medriaas was consumed by the largest dark side nexus the galaxy would ever see.
- Star Wars The Old Republic: Encyclopedia
So not only does this debunk the idea that the Encyclopedia is of a strictly limited perspective, but Bioware itself, with the aid of LFL, confirmed the authenticity of its content by stating such at the beginning of the book.
The Font of Knowledge and Pool of Power being in an entirely different realm negates that conflict, by the way.
Furthermore, Darth Bane: Path of Destruction reveals that both armies destroyed each other in the seventh battle of Ruusan, only resulting in a stalemate between the remnants of those decimated forces. This is what convinces Bane to go straight ahead with the Thought Bomb. So, if they're stalemated, then logically they are of similar numbers, and we know that Lord Hoth went to stop Kaan with precisely 99 Jedi Knights.
Ergo, there's no way in hell that there are dozens of thousands of Jedi and Sith captured within the Thought Bomb. The Wizards article is clearly a victim of a retcon. Drew Karpyshyn strikes again.
Well one can simply look at Darth Nyriss' own explanation of the event, which whilst based on her fallible POV, is nonetheless corroborated by other sources.
She makes it clear that the 8,000 Sith were only the eye of the storm and goes on to state that the Force itself fed his immortality, which is infact repeated by another source.
Now omniscience is incredibly impressive, you're right, but its not the only thing here which can be ascribed as being incredibly impressive. If we are taking his omniscient power at face value, then we have no reason at all to not do the same for the statements from the Encyclopedia, Codex Entries, Holonet info, Bioware staff and more all proclaiming Vitiate to be nigh-Godlike, with immeasurable and unfathomable power. It's stated that the ritual literally changed his state of being. This isn't new.