Hey - I run a naval campaign - done a lot of this Myself.
check out the damage an item rules -
You have hardness and how thick the hull itself is factoring in here to determine HP and a "damage reduction" of sorts.
As far as "AC" - well, objects that aren't attended have a Dex of 0, and thus a -5 penalty to their "AC". You also have to account for the size penalties to determine it.
Usually - the problem isn't hitting the ship - it is doing significant damage to it. Objects automatically take 1/2 damage from energy attacks (except sonic forms IIRC), AND the hardness involved negates "minor" nicks.
Now - with a ship - One of my players suggested a feat similar to mounted combat could be used for avoiding hits. However, I think guiding a horse is a whole lot different than guiding a ship. It might have been valid in some of the smaller vessels - but not what we were using.
Some things players have done for the party vessel/base:
Created magically reinforced hulls and decks -
A laboratory inside an extra-dimensional space, which could
only be accessed ship-board. The priest had a mini chapel where the crew could come and worship every now and then.
Rendered the deck "water tight" in addition to the hull - and took her below the waves...
built a submarine - instead of a ship (this was ELABORATE - using magic, fire elementals to power boilers, generate electricity, generating fresh air via spell - and a whole bunch of wonderful features that only the wizard/gnome engineer could love)
built an airship/extra-planar capable vessel (which was similar to - but not quite like a "spelljammer" - and took the party several years to accomplish)
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The beautiful thing about ships is that the party can move anywhere there is water, sailing around the world, and the GM can scare the S**T out of the party with a mere hurricane, storm, or other natural phenomenon if you catch the party unprepared.
Since that little episode - the wizard has made and put into various locations a dozen control weather scrolls and created a control winds magic item.
The stronghold is mobile - and I find crew are much easier to detail than all the lands surrounding the small city the PC's want to build on land.