Why disable non-core modules when doing a core update?
Contributed modules are not always robustly built and can fall victim to changes made in core. This is particularly an issue if the contributed module has not made proper use of Drupal's API or relies on a database structure in core that may change with the upgrade (even if it is just a minor update). It is therefore safest to disable all the contributed modules before updating in case one of the modules causes the site to fail on completion of the upgrade process. Admittedly this is rare, but it does happen. It happened to us once, but thankfully just on a dev version of a site.