Hi @areaume,
The "species labels" are just a feature we added as part of the RESCRIPt plugin via the --include-species-labels option of get-silva-data. We warn about this under the Species-labels: caveat emptor! Expandable menu in the tutorial.
Although the organism / species labels are present, these labels are not validated by SILVA. At least, as far as we are aware. That is not to say that all these labels are wrong, but quite many do not make sense. Also, there are many cases in which even having the full-length 16S rRNA gene can not disambiguate between species, and sometimes even between genera!
I often will manually BLAST a few sequences to be sure they hit the species I am interested in.
Here are a couple other manuscripts on the topic: