PayPal removed the card payments app due to, according to the app's project manager Christina Li, "something unrelated in our sign-up webpage". Apparently that problem has been corrected. People who had already downloaded the app could continue to use it without any issues.
With its return, both Windows Phone and Windows 8.1 small business users can now access PayPal Here for any mobile payment needs. Keep in mind that Windows 8.1 version still has a 1.9% per swipe fee on eligible transactions in the US, versus the normal 2.7%, until June 15.
Thanks to Chauhan for the tip!