That depends. In the case of the Juncus, there are clearcut morphological differences between the subspecies. One might reasonably call them distinct species. I think those differences are worth noticing and including in management decisions. Some other subspecies blend together so much that I can’t really care.
Keep in mind that the decision to call two population different species rather than subspecies or even population within one taxon is to some extent arbitrary. I mean, the plants don’t care. Biodiversity conservation is about preserving the genetic variation, whatever we call it.