Yes. Your site will incur storage charges even if it is disabled. (Being disabled doesn't take up any less space.)
Daily site charges also continue to apply unless the site is also set to the "Non-Production" billing plan.
Nothing stops you from converting a Production site to a Non-Production site to avoid the daily charge while disabled. But disabling is really only designed to be an emergency short-term measure, so that is an off-label use. If you want to avoid all charges from a site you know you won't need for awhile, it's best to take a backup and then remove it.