It's never been an official index.

This is conjecture but I'm pretty sure the idea of it even being an "index" is a stretch. More like people who work in disaster relief talking about their jobs informally. "I just got back from Town A. They had a tornado but it wasn't too bad. The Waffle House stayed open." "I'm heading to Town B. They've been having flooding so bad the Waffle House has been closed for 12 hours." That sort of thing.

Edit: Apparently FEMA contacts local businesses including Waffle Houses in the areas affected by a disaster to ask how they are doing. This makes sense as an added source of data to gauge the severity of an emergency. Still a stretch to call it the "Waffle House Index".