Is there a good estimate to how many ipv6 prefixes are currently being used?
If by 'in use' you mean 'seen in the DFZ': around 20K. The NLNOG Ring has a nice dashboard on which is summarizes the number of prefixes their lookingglass receives from members. As you can see here, just over 20K prefixes can be seen there.
There's no single correct answer here, it all depends on the filter policies networks and their upstreams use and how all networks on the internet are connected, but it's fair to say that 'around 20K' is a good approximation.