Is it OK to use Blast+ to query NCBI's 16s rRNA database with 16s DNA sequences?
Your confusion is understandable, since it isn't explained in the NCBI description of the database, but most of the sequences in the database are derived from DNA that encodes the 16S rRNA gene, not from the rRNA itself. In some cases, sequences are derived from cDNA that is synthesized using the actual rRNA as a template, but it's still DNA sequencing. Direct RNA sequencing is extremely uncommon. Depending on the cDNA sequencing protocol (first strand vs. second strand sequencing), the transcript sequence might be the reverse-complement of the 16S rDNA, but the only difference that you would see is that the numbering of the bases would be reversed. If you are sequencing rDNA from organelles, there may also be a few bases that are different, due to RNA editing.