Thanks @ebolyen. Unfortunately, @Aishiki's results fit with our latest test results.
We are currently recommending that users avoid using classify-consensus-vsearch for more than tens of sequences.
Fortunately, classify-consensus-blast gives very similar performance to classify-consensus-vsearch in terms of accuracy, but in our tests runs 50 times faster. If run time is still an issue, classify-sklearn was 500 times faster in our tests. There is a tutorial for how to use classify-sklearn here.
We haven't had a chance to look at why classify-consensus-vsearch is so slow. @Nicholas_Bokulich may have more to say on this in future.