A
possible work around for missing ships is the following; Take your ship rune and remark over it, so it goes from original Red to a Gray rune. I lost my ship a few times with the original rune, but I've been fishing non-stop since Saturday, putting in about 8 hours a day, recalling away every time my backpack got full, and I've not lost it since.
Of course, I could also just not be being hit by any of the bugs, which may not have anything to do with the runes at all.
Back to the main topic, I did manage to find Sienus' boat for him today, also near Moonglow... mostly because I've kept running into it
So one other suggestion is to check your last plotted map path, and see if your boat is anywhere along it. Also get the Enhanced Client; I know many of you hate it, but you'll find the enormous zoomed out view handy; sailing along the main routes between cities I've seen about 30 different boats in the middle of the ocean, but I'm not sure how many of them are "lost". I'll try and start writing them up as I go if anyone thinks it'll be useful...
Unnamed Ship (Gargoyle, Light brown/yellow trim paint scheme): Piloted by Neil. 71.27N 168.49E (North of Nujelm)
The Trinsic Fishing Vesle (sic) ((Gargoyle, Light brown/yellow trim paint scheme): Piloted by Sheila. 72.56N 152.22E (North of Nujelm)... This Structure Is Somewhat Worn.