What is the proper way to uninstall a module that adds a content type
You should not delete content types in hook_disable(). Instead, you should make sure callbacks are left sane, and all data you will need on hook_enable() is properly archived and secured from modification by other modules. Good idea is to use drupal_set_message() to warn about content type that should no longer be used or displayed, but that's site admin's responsibility.

On hook_uninstall() you are supposed to left the database as if your module was never there. Thus, feel free to delete content types that was created using node_type_save(), if there are any. The ones created with hook_node_info() will be deleted automatically. Again, setting message about orphanted content is good idea, but it's site admin's responsibility not to uninstall module he is still using, after all.

If your hook_node_info() defined content type is not deleted, just disabled, you can decide to explicitly delete it, but you are responsible for cleaning all the mess it may cause, like orphaned content. You risk serious site failure if you don't.

Edited to incorporate information from Clive's comments under other answer