I think it was mostly due to voter fatigue mixed with new storylines and perhaps some voters thinking they would shift their higher Vezina vote for Hasek over to just the Hart.
Hasek already did the borderline impossible by winning the Hart and Pearson the previous two years, so even though he was even better, he was not only competing against the field, but his own elite standards and the perception of, “yeah but we’ve seen this already the past couple of years.”
We see it a lot in sports. The NBA leaps to mind with players like Jokic and Nash missing out on three straight MVPs, despite outperforming their prior two. With a position specific award like the Vezina, perhaps voters wanted to spread the wealth a little more, thinking Hasek would win no matter what, as he ended up doing.
We should also consider that Dafoe played especially well down the stretch for the Bruins and helped propel them into the playoffs. Maybe out-dueling Hasek in the final game of the season to win in OT to avoid the 103 point Senators in the first round made a voter or two extra enthusiastic.
While there were a number of other reasons Toronto made a big jump in the standings, Cujo was the main reason why. 1998-1999 was his first season with them. His numbers don’t exactly scream Vezina runner-up, but that’s where perception can come into play.