Comment 33 for bug 968533

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:
https://addons.mozilla.org/en-US/firefox/addon/bookmarkmenuhider

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 :-(