Hi,
If you use a payment plugin like "collect on delivery" you can specify an order status for the order, just after his creation.
So using this plugin you can say that the created orders will have the status "pay later".
After that, HikaShop allows users to pay unfinished orders. You have to activate this option for that but it is possible.
There is also an option to list the order status for the unfinished orders, option where you should add your "pay later" order status.
Thanks to it, in the order listing of the user panel, the user will be able to see his orders and his unfinished orders.
A dropdown will propose him to select the payment method and pay the unfinished order.
About the email, there is generally a link to the order in the website. You can see to customize the email to put a conditional link (depending the order status) so the customer will have a direct link to the order listing with the payment selection.
Regards,