In order to override Hotel Booking plugin files from wp-content/plugins/motopress-hotel-booking/templates/ folder you should copy them to
/wp-content/themes/your-theme-folder/hotel-booking/ directory. Thus in your case you should go to your theme root folder on your server and create /hotel-booking folder. Then open just created /hotel-booking folder and add /shortcodes folder. The open /shortcodes folder and create /search-results folder, etc.