I was just wondering the same thing.
My theory so far is that those results were indexed before the change in settings being done.
I'm thinking if I ask for a new indexing it might work.

UPDATE: YES - That was exactly it. I followed instructions and went to Spotlight preferences in the Privacy tab. I added the Applications directory to the list of removed content. The Applications disappeared from the Spotlight results. Then I just removed Applications from the exceptions list. It was instantly re-indexed and all the results didn't have the ".app" extension anymore.