The schema file is here for generating/creating/editing options for your theme which will be displayed in theme interface for user. It is the one you use to create options (setting all parameters such ID, type, label, etc...).
The data file is recording all option values. It's sort of database in JSON. It might be used to modify an option value or a theme preset directly in the theme without using user interface.
Schema manages keys and data stores values set by user.