So you can’t define a keyboard shortcut for launching your bookmarklets in Chrome. But you can set a keyword shortcut for quick launching from the Omni Bar.
For example: I’ve added my MarsEdit bookmarklet as a “search engine” and defined its keyword as “m”. Now I can bring up a MarsEdit post linking to the webpage I’m on by: hitting CMD+L to go to the Omni Bar → typing “m” → pressing Return. Not as convenient as just hitting CMD+2 like I do in Safari, but it does beat using the mouse.
(Thanks for the tip, Dan.)