If you set up a wiki farm as explained in Manual:$wgConf, the update.php script will stop working for you because when you run it it has no way to know which wiki to update. There are several workarounds you can use, but none of them is simple.
The simplest solution is to allow update.php to accept a parameter called domain, which would then be used by the script to determine which wiki to update. That would simplify the process of updating each wiki in a wiki farm to running something like:
php update.php --domain=SUBDOMAIN.DOMAIN.TLD
This would require modifying the update script to accept and consume the parameter, modifying other pieces of the code to allow for selecting a wiki based on that parameter so the correct config is loaded, and modifying Manual:Update.php to reflect these changes.