It most likely means that the Queen is at Balmoral Castle. You can always tell these things because the Royal Standard is only hoisted when she is in residence. It's also an indication that the vote will be no, as she certainly knows, and would be most likely to be in Scotland when a no vote is announced.
If Scotland leaves, it will have to decide on keeping the Queen (like Canada) and joining the Commonwealth - so she should show the flag whether they stay or go with the UK.
That normal time of the year for the Queen right