You only run
[cmd=#]portsnap fetch extract[/cmd]
to initially populate your ports tree. To update it anytime thereafter run
[cmd=#]portsnap fetch update[/cmd]
It won't hurt anything and you want to keep it up to date as you install programs. I run
# freebsd-update install[/cmd]
after I've installed everything, but am already up to date at FreeBSD 9.0-RELEASE-p3 if I run it now. As to whether or not it could cause a problem there is at least one thread addressing problems that it has caused lately , but it's never caused one for me.
On the subject of updating ports, just in case you weren't aware of it, it's essential to install [file]/ports-mgmt/portaudit[/file] and to run
on a daily basis to stay current on any vulnerabilities, then use [file]/ports-mgmt/portupgrade[/file] to upgrade any ports that it lists as having a vulnerability to the newest version, making sure to update your ports tree before you do so.