Yes. Normally, if they have provided their paypal email address, when you click on the pay button, you'll get a popup which will ask you if you want to pay them via PayPal or by another mean. If you select PayPal, you'll be redirected to PayPal and you'll have to validate the transaction with your own PayPal account (like if you where purchasing something from them).
If you select that you want to pay them via another mean, HikaShop will just create the entry in the database and reset their affiliate payments but it will be up to you to send the money to your partners the way you want (like for example by doing a wire transfer at your bank).