Each ship is it's own separate instance, which is why you'll see people on Stormbolt:27 or whatever when you're searching the who list. When you leave the instance it resets in a couple minutes just like a quest.
Also if you're having bad lag, you can click the portal door twice and accidently be sent to an empty ship.
I don't agree so much with the interior design aspect. I don't even mind running below deck to get all the buffs. But I would like to name my guildship. Putting up a board with guild rules or upcoming guild raids could give a long term message, without bumping off the guild message of the day.
As a guild leader, I would like a few abilities. To see what 'in guild alts' a person has, so that if I see someone has been inactive for a couple weeks, I don't drop them if they have been leveling a different toon, in the guild. I would also like to give ranks to my officers. Maybe even make a list of guilds that help us out or that we've been helping. That's just my two coppers worth