So there are still molecular biologists who call similarity "homology"... no, people. No. That's not what homology means.
Then fill me in. What does 'homologous' mean? If all 16S rRNA genes have a shared ancestry (and they do), why are they not homologous?
Phenetics is based on overall morphological similarity, which doesn't work for prokaryotes (at least not for higher-level classification) where external physical characteristics are a poor indicator of shared ancestry (as assessed by 16S rRNA sequence identity). Physical characteristics are encoded by genes, and genes are prone to rampant lateral gene transfer. Cladistics would also not apply, for the same reason.
The phylogeny of archaea and bacteria is based principally on the 16S rRNA gene. Using the phylogeny of the 16S rRNA gene as the basis for prokaryote classification (and life in general) is neither phenetic or cladistic. This applies to any molecule-based phylogeny.
To be honest, I don't know to what extent PhyloCode could (or does already) apply to the classification of bacteria and archaea.