Here's the first cut at it. The colored numbers are one axis of the matrix. This can be a d6 roll, an aspect, or a combination of the two.
The color sections indicate segments and the colored numbers indicate the hex row to follow. Roll one die (in this example) for segment and another for row number.
Let's assign the blue numbers to a roll of one. If you roll a one on the segment select die and a 2 on the hex row die you move down the grain until you hit the first filled hex. This is a B indicating a bridge hit. Apply damage to this box, either marking it out or adding a tick mark if your boxes take more than one hit to destroy. If this box is marked out, a subsequent hit will penetrate thru the destroyed hex to the Q hex directly below.
This is way rough yet, and this design is not optimized, but it should give a feel for what I have in mind. It would be more elegant with a 10 or 20-sided die, but d6 works well enough for this example.
Ship size doesn't matter. Any ship you can model on a 6 by 6 grid as Dan did will fit in this matrix. The only difference would be the damage value of the individual hexes. A large ship would require several hits to destroy a hex, a small one might have several hexes destroyed by a single hit.
As I said, it's rough, but if there is interest in this, I'd be happy to work with anyone interested in refining it.