Well, just to put my 2 cents in
Your navs will not enter terrain that is too tall for the ship, so that is not
a problem. Also, the weight of your cargo hold has no bearing on ship height,
despite the 'real world logic' that might be involved; it's too minor of an
effect to be worth the coding or the waste of CPU cycles.
It sounds to me like this was just a particularly unlucky situation (which can
be avoided with some care). Ships take some small amount of damage when
moving, more so when they are just barely scraping along the treetops or
mountaintops. So, most likely you entered the mountains because your ship
actually could fly over them, gave a warning message about not clearing the
terrain well, took movement damage, and crashed. Considering your typical
class 3 hull has ~10500 hit points (not that the absolute number matters much,
since players and ships operate on different hp scales...), and movement does
~10 damage on a <really bad run>, this was just unfortunate timing.
Am I going to make it so that your ship will not sail under these risky
conditions? No. The reason being that you are the captain, and if the ship is
physically capable of doing something, the crew will obey you (some quote
about absolute power might be appropriate here...). In addition, you can
avoid this issue in a variety of ways (playing with the height lever, paying
closer attention to your hull condition, getting more lift magi, avoiding
mountains or other 'borderline' terrains for your ship), while in some
situations running that bit of risk might get you away from an enemy (Would
you like to stop running from a monster that is beating up on you, just
because you'll lose some hp for being out of ep? not exactly the same, but
not too dissimilar.)
Melemkor
Of course, if there was a bug involved, I would look closer at the issue (and
indeed there was a similar bug some months ago that was fixed). However,
unless someone can show that this was not an isolated incident, I am inclined
to assume that no bug was involved.