Again, losing masts is a common factor in this kind of warfare so again bad luck if your on the receiving end, there is one factor missing in all of this which has not been programmed in yet though I'd expect it to be a critical factor in an engagement which I note in paragraph 2.
The Santi for example on both occasions struck her colours due to losing her masts. Its a typical and acceptable form of attack on large ships and usually a dismasted ship signalled an end to that ship's engagement in the battle and an expectation of colours being struck when challenged. This was a kind of acceptable form given the immense sums of resources to field them and the temptation of the prize in their capture. No Captain really intended on sinking, only to neutralise, secure and move on. Hence why dismasting is such an effective tactic.
Colour striking if anything is missing immensely in this game testing so far, it should be the form to which an engagement ends rather than everyone just sinking everything. Taking the Prize was more important and valued, sometimes sinking was very important, for most of the time though preservation of your crew and your ship over ruled a fanatical death wish. This is where the AI needs to improve too for factoring in morale for them as well as your own crew's morale as a risk factor when certain kinds of damage events occur on your ship.
At Trafalgar HMS Africa got a little too eager when seeing the trouble the Santi was in, the Africa was the smallest (64 gun ship) in Nelson's fleet and mistakenly assumed the Santi would strike her colours as they came alongside and began the formalities. The boarders were informed that the ship was still in action and asked to leave which they did.
Despite this the Santi was effectively neutralised. She had been neutralised before in the past having being dismasted in the battle of Cape St Vincent in 1797 where she was lured away and set upon by smaller ships. They failed to secure her as finally other Spanish vessels arrived on the scene despite her striking her colours knowing full well it was pointless to continue.
Despite a little ship not being able to penetrate the hull, its the fact you are dead in the water with hundreds of mouths to feed with no means of returning to any land that motivates you to surrender and therefore have a chance in seeing a new day being towed back.