As of June 2016, another reason for the missing VLQ flag option is that the post (question or answer) is older than seven days. If a post sticks around for 7 days or more, chances are very high that it's not very low quality:
but the truth is that very few VLQ flags ever get raised on posts over 7 days old... Heck, 87% of all VLQ flags are raised on questions less than one day old. The vast, vast majority of the worst cruft gets cleaned up quickly...
The Very Low Quality flag option is also unavailable on questions which are already in the Close Votes review queue; since the 'negative' outcome of a Low Quality Posts review on a question is to close it, it's pointless to review it in two queues.