Same thing happens to pirates. They get blown to pieces without trial. An enemy combatant has different rules than run of the mill criminal.
Sure. So the US is acting much like a third world country, right?
When it comes to identifying who to bomb, I'm sure there are protocols.
These are assumptions, as are your list. There might be no such attempts. And, if it came down to it, there is nothing to stop them just capturing the same boat. As said, it is uncivilised.
But the thing is, people want to see "the other side" punished, in what ever form that takes. That is not the way I think. The "other side" is a stupid position.
You're not wrong. It's possible there might be no attempts to capture the enemy before blasting them to pieces.
However, I think this is unlikely. Military, at least US military, are given rules of engagement for combat, such as "do not fire unless x, y, and z conditions are present". Failure to follow the rules is punishable. Furthermore, the Navy is tech heavy. Their combat situations produce a ton of data through video, radar logs, communications recordings, intelligence, and such. With their decisions and actions on the record, it's reasonable to expect they'll follow the rules of engagement. They tend to be very disciplined, and cold, when it comes to destroying a target.
In my opinion, it's a much bigger assumption to think these are bunch of gun toting yahoos meting out vigilante justice.