You should never change the database structure,, if you just wanna display the short description in place of description there are hooks and filters you can use alternatively you can override the plugin file that displays the single products by creating a woocommerce directory and add tha file in the same hierarchy as in the plugin templates folder.
have a look at https://docs.woocommerce.com/document/template-structure/
you’ll also going to find the hooks and filters to do the job if you dont want to add the woocommerce directory.
you need to update the yourprefix_posts table, the products are also wordpress post you can write
update yourprefix_posts set post_excerpt=post_content , post_content="" where post_type="product"