Good news my fellow Starbound brethren! The latest hotfix patch has solved the case of the mysterious vanishing ship lockers and fuel hatches, and we know that it works thanks to a quick test done by our own Digmbot (who backed up his saves anyway and tried the hotfix on a save he intentionally messed with).
Among many other bug fixes, the fact that this hotfix has stopped ships becoming unplayable by removing one of its most important (and irreplaceable) elements means that it should finally be safe to update your Starbound game to the Enraged Koala beta and begin reaping the rewards of Valentine's Day themed items, tameable dogs and a microphone voice by Smooth McGroove. Strangely even though the hotfix notes say that ship lockers and fuel hatches that had been erased could not be restored using this hotfix, Digmbot was able to get back his after applying the new patch and opening the game he'd had his locker and hatch erased from so in a few cases it might be possible to get them back still. Don't hold your breath though.
We would still suggest backing up your ship and worlds, just in case something else unforeseen happens and the folders you need to make copies of are highlighted in the image below (once again, information provided by Digmbot).
Hotfix patch notes are here.