Well, you did tell the system you don't want those applications anymore.
Deleting them marks them as Hidden which makes nautilus, the menus, and
gnome-session completely ignore them.
However, in a future release of alacarte you will not be able to delete
things at all (because people don't realize it has these kinds of
effects) so I guess that'll "fix" this bug.
** Changed in: alacarte (Ubuntu)
Status: New => Invalid
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Removing unused applications via alacarte results in unusable desktop
https://bugs.launchpad.net/bugs/378422
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