Same problem here, though it seems it have worsen recently on 13.10
(with Firefox 25?). With 5000 bookmarks, hud-service uses one CPU at
100% all the time, with a complete freeze every-time I switch a tab or
firefox's window gets the focus.

By using the BookmarkMenuHider add-on to remove the bookmarks from the menu, 
the CPU usage goes back to 20% the time. This can be a nice workaround for 
computers with relatively beefy processors. You can find the add-on there:

Finally, the "ui.use_unity_menubar =  false" fix drops the CPU usage of
hud-service below 1%, and Firefox experience is back to butter smooth
:-) Of course the drawback is that the menu is gone from the HUD :-(

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  Alt-tab to Firefox sends Firefox to 100% CPU; unity-panel-service to
  80% CPU and hud-service to 20-80% CPU

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