"Your theme has bundled outdated copies of WooCommerce template files"

Hi,

Yes, you can copy the WC template files into theme folder.

Here is the resource you can review https://docs.woothemes.com/document/template-structure/ for overriding WooCommerce template files.

I hope it helps.

This is something you need to contact your theme author about. Most likely copying it over will not work correctly because your theme has probably modified it. So another words copying the default ones over will get rid of the message but may break your layout.