Hi Dee - I don't recall ever disabling anything before upgrading. It is a good idea to take your site offline temporarily while upgrading Joomla! or major components, etc.
Regarding your other question about 'simple scripts' being the same as a 'manual upgrade', I think I understand what you are asking. Personally, I have never (and likely would never) use any script to upgrade a Joomla! installation. It is so simple to perform an upgrade via FTP or many other file managers.
The biggest concern I would have when upgrading a complex site with lots of extensions or customizations, would be a concern that: a) those items currently installed were compatible with the latest version of Joomla! I was going to install and b) I might overwrite any code hacks previously made to core files.
So, when upgrading, especially on complex sites, ALWAYS do a complete backup of the site, database, uploaded files, etc. On my hosting, there is a backup of each site done every day, so if something goes south, I can restore everything in seconds back to the last backup.