Help is broken in Aperture 3 because Apple, in their infinite wisdom, disabled JavaScript (by default) for the HelpViewer application on Snow Leopard (but not on Leopard or Tiger).
This has nothing to do with whether or not JavaScript is enabled in "Safari"
This lack of JavaScript also affects Finder and iTunes help, although to a lesser degree. Those apps only use JavaScript in their "Index" pages (which is why the alphabet bar in Finder or iTunes help doesn't work on Snow Leopard).
You can re-enable JavaScript for "HelpViewer.app" by typing the following into the Terminal window:
defaults write com.apple.helpviewer WebKitJavaScriptEnabled -bool yes
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