Performance: is preferable to use Rules or node_presave/node_save/other hook ?
In practice, it is far easier to debug a hook than a rule that includes a PHP function.  So, not only are hooks faster, they are easier to maintain and less likely to present security risks.

You do not need to remember "in which module foo happens" if you put all your hooks in a single custom module for the site.  Unless you have an extremely large number of tweaks, using a single module (and version controlling it!) is probably the easiest way to do this.

Regardless of the size of the site, if you want to write custom PHP, you should use a custom module, not rules.