Possible solution?
I've been having this problem too, but I think I may have found a solution.
I'm not sure if they were disappearing on every reboot or just frequently on reboot, as I would only notice it when it happens.
These aren't icons not in a widget, these aren't apps on SD cards etc. Just Gmail and Google Maps, preinstalled on my phone, and placed as icons directly on the homescreen.
It occurred to me that maybe it's related to the fact that the apps also have shortcuts in a "Google" homescreen folder. (By folder I mean the icon group that get formed if you drag one icon onto another.) Maybe the phone either
a. does an icon redundancy check on start, sees that the icons already exist in the folder, and deletes the non-folder copies? Or maybe they
b. somehow never get stored to begin with the long-term registry or whatever, if they exist already in an icon folder.
I just tried deleting the shorrtcuts from the "Google" shortcut folder to see if that stopped the disappearance. (Actually I deleted both copies -- folder and non-folder -- of each, then re-added them back to the homescreen, just in case it's "b", a failure to save the change in some persistent registry at the moment that they were originally added to the homescreen.) Then I rebooted.
So far, so good- after the reboot they're still there. So I think this may be a bug related to having multiple shortcuts for the same app. Look around to see if you have any duplicates of the shortcuts in a homescreen shortcut folder.