The release of version 1.7.0 for WC Pickup Stores is now including a tax handler that will allow the site’s owner to enable the taxes for store pickup shipping, enable taxes per store, or disable taxes completely when pickup store shipping is chosen.
Now, if your site has taxes enable for WooCommerce your WC Pickup Store settings will add a new option to set the tax status.
One of these new options will allow you to enable the tax calculation only by stores. This setting will add another option to the store admin page, in the Miscellaneous section. Enable this if you want to enable taxes for this store.