I had the exact same issue, however it was a different cause. Since googling for "aperture keyboard shortcut quit working" returns this page as #1, I thought I'd document what fixed it for me.
I had installed 1password. An otherwise excellent program, but it registers its keyboard shortcut in a way that it doesn't show up in Keyboard Preferences, but it is active absoluetely everywhere.
Here's how I found out about it for others to troubleshoot: I opened console. Every time I pressed command-\, I got the message: Failed to send 'activate' to 'com.apple.Aperture', client not connected. The logging program was called "1PasswordAgent", so it was simple to figure out from there. Add this to your box of tricks when things aren't working - look in Console.
Anyhow - after I got rid of that keyboard shortcut in 1password and logged out/back in, my Aperture keyboard shortcut started working again.
Hope that this helps someone else in the future. If so, please reply to this post to keep it the #1 search result in google. 🙂