Even though I've explicitly set the Finder preference to display all file extensions, I'm still finding that some apps do not show the file name extension in their Spotlight result.
Here are some examples.
I'm running Mountain Lion.
It seems this happens when Spotlight indexes the apps before the setting to hide extensions was in effect. You should try reindexing applications to resolve this issue.
Go to the Privacy tab in Spotlight preferences and add the Applications directory to the excluded locations. This should remove all applications from the Spotlight index. Then remove it again from the excluded locations so Spotlight will reindex applications with the correct settings. After reindexing the ".app" extension should be removed from all results.