How can I systemwide check if a keyboard shortcut is in use or has been registered? How can I query OS X to know if an application has registered a shortcut?

I could inspect every app I have or that is running at least with KeyCue and go through the Keyboard Shortcuts section of System Preferences, but there must be some other method using the shell.
/usr/libexec/PlistBuddy -c "Print" ~/Library/Preferences/com.apple.symbolichotkeys.plist


Will do it for you. Then you can edit the individual keys from there.

The details are extracted from:
http://reviews.cnet.com/8301-13727_7-57337941-263/tackling-keyboard-shortcut-woes-in-os-x/

You can modify the above file as per:
http://support.apple.com/kb/HT4850

However note the file is binary and you cannot use a text editor, you have to use the command defaults, or the command PlistBuddy.  defaults can be used if you know the individual keys you want to modify.  PlistBuddy is more user friendly.