16S V3-V4 length : what to do with the sequences of shorter than expected length after DADA2?

Oops, sorry I forgot to embed the link. Here is the trick for the length filtering.

Better late than never! Certainly worth challenging that notion in most cases.

Not really, to me its basically picking the worst of both worlds, but that is another topic on its own and unrelated to this one. For your interest, several reading materials collected in this thread.