Short answer: yes.
Long answer:
The Customize API uses one of two methods for storing customizations: the Settings API or the Theme Mods API (the latter being the default method). Thus, all changes are saved to the database, either as a Theme-defined option, or via theme_mods_{themeslug}.
When the Theme is updated, the Theme files in /wp-content/themes/{themeslug} are deleted and replaced, but the database entries in wp_options remain untouched.