Mac – Disable F3 and F4 shortcuts

You should take a look at Function Flip. It can selectively toggle function keys between being regular function keys or the special hardware keys, including the media keys (F7, F8, and F9). Essentially, it does the same thing as "Use all F1, F2, etc. keys as standard function keys" setting (System Preferences > Keyboard), except only to individual function keys instead of all of them.

You can edit the plist directly:

defaults write com.apple.iWork.Numbers NSUserKeyEquivalents '{"Add Column Before"="\0";"Add Column After"="\0";}'

It overwrites custom shortcuts set in System Preferences, but you could also edit the plist in a text editor after converting it to XML:

plutil -convert xml1 ~/Library/Preferences/com.apple.iWork.Numbers.plist