I do not know how to assign a keyboard shortcut to a menu command that doesn't already have one (or even how to change one in Numbers 3).
Hi Ian & wideEyedPupil,
I don't know about assigning a keyboard shortcut where already one exists (because it might create a conflict) but it is not hard to assign a keyboard shortcut to just about any menu item in any Mac app that doesn't already have one assigned.
Fire up Automator, create a new Service, drag a Run AppleScript action into the right pane (set it to receives 'no input', paste a "GUI" script into the action, and save the service in your Library > Services folder. Then assign a keyboard shortcut to the newly created service in System Preferences > Keyboard > Shortcuts.
The script that would go in the service for Autofill Down (replacing all the default code that Automator suggests) would be this:
my do_submenu("Numbers", "Table", "Autofill Cells", "Autofill Down")
on do_submenu(app_name, menu_name, menu_item, submenu_item)
tell application app_name
tell application "System Events"
tell process app_name
tell menu bar 1
tell menu bar item menu_name
tell menu menu_name
tell menu item menu_item
tell menu menu_item
click menu item submenu_item
on error error_message