Filter Controls or Not to Filter Controls

That approach was fairly specific to the quality filtering / OTU picking strategies available in qiime1 circa 2012. A lot has changed since then, most notably denoising methods like dada2 for Illumina data that perform more sophisticated methods for eliminating spurious reads. This thread has some more discussion of the abundance filtering methods in qiime1 (and the original paper benchmarking that approach) and whether or not they are appropriate with dada2 (probably not, but it's untested).

So no, I would not recommend performing an abundance filter after denoising with dada2, unless if such an approach is validated by benchmarking on useful datasets.

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