Spend 40 or 44k on a "living figurehead" (Stormwrack) of a black, green, or copper dragon (depending on the alignment you wish to feign and the nominal mood you want it to express.) It can function once a week for 10 minutes, but gets your ship an adequate breath weapon and complete immunity to acid. Or buy a planar helm for a 2x Planar Navigation on the ship, and just take a vacation in celestia or equivalent while the storm passes (where the spell targets the ship to and from is left as an exercise for the reader.) Or spend 10k using the stronghold builder's guidebook and turn your ship into a "zone of elemental immunity."
With that said, you're epic, so epic spellcasting can trivially have a spell named "protect a ship against acid, or rather 'convert all acid in 100 miles into minty-fresh spring water' or "kill the gentleman making this acid" or "create sufficient oxidizer or base within 1000 miles to bind to floating acid and neutralize it" (call that one the snow of baking powder) "
Presuming the acid storm is indeed acidic, take a bag of holding (of maximal capacity), fill it with baking soda formed by using polymorph any object on bags of chalk dust (mineral -> mineral of same size and class will be permanent), cast energy immunity (or resistance) on yourself, fly to the heart of the storm, start dumping bags of baking soda into the storm. Use gust of wind spells to distribute it. Given the capabilities of epic parties, this process (or the reverse if the acid is a base caustic called "acid" by the natives) will sufficiently annoy the originator of the acid storms that you can have the inevitable fight with it and resolve the problem in the time honoured adventurer fashion.
However, you don't need to use epic spellcasting. Hardening (spell compendium, page 109) provides an increase in an object's hardness by 1 per every other caster level. A ship, (presuming the ship itself is non-magic), has a default hardness of wood, or 5. Presuming that you don't simply coat the ship in glass or, being epic, adamantine, that provides a 5+(21/2) hardness sufficient to deal with 15 acid damage. You can use the normal means of increasing caster level to provide a hardness that you desire.
You'll need better sails than cloth (assuming no tricks with circle magic or other caster-level increases), but again, being epic, having mithral sails is completely reasonable (or you can simply upgrade to suitably epic means of propulsion).
Depending on the nature of the acid (what kinds of substances does it react with?) you should probably polymorph-any-object the wooden planks of your ship to either adamantine, mithral, ironwood, gold, or deep crystal.)
Any kind of "real bases" , berths, or docks, that you expect to suffer from this acid-storm should be protected by permanent prismatic walls. Note that unlike other walls, prismatic walls don't have the (S) shapeable descriptor. you'll need to have the sculpt spell metamagic to make a proper conic roof. Still, it's worthwhile due to the spell/object immunity it provides.