pm-updatecode updates the code of your installation. In a multisite install, all sites share the same code, so if you run pm-updatecode on one site, you have updated the code for all of the sites.
After you update the code for a site, you must update the database. This is done with the updatedb command. If you run pm-update, it will first run pm-updatecode, and then will run updatedb. However, this will update the database for only one of your sites. You will then need to run updatedb on all of the other sites in the multisite install.
Note that between the time you run pm-updatecode and the time you run updatedb, your site might not behave correctly; it is therefore advisable to take a site offline when updating it.
In a multisite install, then, all of the sites must be updated at the same time. It is therefore better to stick with single-site installs, so that you can handle updates on each site one at a time.