Yes, portals can be deleted. Recently in Germany all 2nd world war concentration camps have been cleared of portals. This is a rather unusual case though. But portals can be deleted by reporting them.
If you feel a portal is against the rules (e.g. I have seen grass and standard road markings...), is removed from the real world or is in a dangerous location, you can repotreport it to Niantic:
- In the scnannerscanner app by tapping on the image, then hit the "Edit" button at the bottom and then you'll find the option to "report invalid portal".
- On the Google support page (might go away soon now that Niantic has departed from Google): Click "Contact Us" in the top right corner, then "Report an issue with a Portal or a Mission" and then select a reason.
While the portal is removed from the game world, I believe your stats (unique hacks & captures) will not be decreased.