This change is intended. Laurent had never meant for s6-envdir to ignore directories, the previous behaviour was just a coincidence. When I made him asked him about this last week, he immediately made the parsing code in skalibs stricter.
To be more precise: the fact that directories were being ignored was a consequence of a bug in the implementation of openreadnclose. Fixing the bug changed the behaviour of s6-envdir, but the new behaviour is the one that had always been intended. Sorry if you relied on the previous behaviour. I will add a note about the contents of an envdir. -- Laurent