I'd do it afterwards as there's a risk there's some confusion where the configuration files should end up (they need to be moved from /etc/named/ to /usr/local/etc/named/) if you install BIND from ports on 9.3. On FreeBSD 9.3 BIND (from ports) will start using the system's /etc/rc.d/named script, on FreeBSD 10.x it'll be from /usr/local/etc/rc.d/named. The scripts are slightly different and would cause a lot of confusion.Since 10.3 no longer includes BIND, should I move to the BIND 9.9 pkg before or after the OS upgrade?
Yes, very likely. At the very least make sure you have a good backup of /etc/named just in case.Will the OS upgrade delete my existing named config directories?
I'd do it afterwards as there's a risk there's some confusion where the configuration files should end up (they need to be moved from /etc/named/ to /usr/local/etc/named/) if you install BIND from ports on 9.3. On FreeBSD 9.3 BIND (from ports) will start using the system's /etc/rc.d/named script, on FreeBSD 10.x it'll be from /usr/local/etc/rc.d/named. The scripts are slightly different and would cause a lot of confusion.
Yes, very likely. At the very least make sure you have a good backup of /etc/named just in case.