I had the same question a while back and made use of this excellent post from the maintainers. Quoting from there:

However, it [Kraken2] has a tiny false-positive rate (erroneously assigning a read to a species) that KrakenUniq does not have. This means that for diagnosis of infections, where the goal is to identify a very small number of reads (often just a few dozen out of millions), users should use KrakenUniq.