RAW, Lightning Bolt only immediately damages creatures.
Spells (or portions of spell effects) that are explicit about affecting creatures mean that, by default, non-creatures are not affected by those portions of the spell.
As you quote, the portion of Lightning Bolt that causes immediate lightning damage only does so to creatures in its line of effect; they make a save, and the amount of damage is based on the save. Since the ship is not a creature, this entire section doesn't apply to it; it doesn't make a save, nor does it take any portion of the 8d6 lightning damage.
However, the ship is still potentially set ablaze as per the next part of the spell:
The lightning ignites flammable objects in the area that aren’t being worn or carried.
This is not tied to the above section about making a saving throw and simply happens to any applicable objects within the Lightning Bolt's area, no save required. As such, so long as the ship is considered flammable (and unworn and uncarried), it should simply catch fire wherever the Lightning Bolt's area of effect overlaps with it.
(Do note that it may not be considered flammable, depending on its condition; wet material doesn't burn easily.)
That said, I recommend talking to your DM about the specifics of how this works in their campaign; it is not at all uncommon for DMs to allow "creature-only" spells to affect objects in some way. In addition, it's not uncommon for DMs with specific campaign themes (such as being aboard ships for the majority of it) to have specific rules for what works, how it works, and what doesn't work when interacting with them in order to avoid situations where, say, a common spell is an instant ship destroyer.
In regards to whether or not you can aim the Lightning Bolt to attack the sails in the first place, Area of Effect spells like Lightning Bolt, Fireball, etc. generally don't care whether or not an affectable target is present within them; you're free to place them wherever you like, regardless of whether or not there's anything to affect in the target area. Single target spells, on the other hand, get a bit weirder.