A lot of "disappearing" boats were launched before Publish 70.
IF any of you have ships out there that haven't been dry-docked since march or earlier, you need to unload it, dry-dock it, then relaunch it.
There was a fix put in publish 70 that was to fix it, but it didn't fix ships already in the water. EDIT: NOTE THAT GMs ARE ANSWERING PAGES ON MISSING SHIPS, AND WILL TRY TO REUNITE YOU WITH THE SHIP.
This is related to the bug that kept pirates and fish quests from being delivered.
If you have active fish quests, and can't get the fishmonger to recognize your ship, bring the ship in, park it, launch a second boat at the docks, deliver the quest, DO NOT get a replacement quest, and then drydock the second boat. Repeat until you have no quests active. Then, you can drydock without losing reputation.
Of course, there is the possibility that the fix wasn't a complete one, but I've not yet seen a ship launched after the fix that went missing from just its runes stopped working, but had help (like being left at the docks too long, and getting relocated by the timer, or being left where other people could move it), or hadn't been properly refreshed (some people had the mistaken idea that just visiting the ship refreshed it, when it takes clicking on the ropes or the pilot to do so).
The best way to find a missing ship that hasn't decayed (without waiting for a GM) is to have a couple friends. You place a new boat (or pilot another friend's boat), then have your friends move their boats to where they are barely on the edge of your in-game radar. Then, you all sail sweeps together over the area where your ship went missing. Get 4 or 5 friends to increase the search line, and you can cover twice the area.