Best practice for custom module variable names?
It is possible to use a Drupal variable to contain an array; that is what Drupal core modules do too (see book_type_is_allowed()).

It is possible to use a single Drupal variable to contain different settings used by a module into an array. With the form #tree attribute is still possible to use system_settings_form() to save the array into a Drupal variable without writing any additional code. Serializing the de-serializing the code is automatically done by the Drupal core functions that handle Drupal variables (see  the code of variable_set()).

The question is then: when should a single Drupal variable be used to contain different settings? I would use a single variable for settings that are used by a function, or a group of functions; if the array contains values used by (for example) 10 different functions, but those functions access a single value (or a couple of values) from that array, then I would not use a single persistent variable for the settings.