How does pirates commandeering/ransoming ships affect the different links in the chain? Who is protected and who loses?
Most pirates around the world are petty thieves. However you are probably referring to Gulf of Aden pirates, and they don’t “commandeer” so much as ransom, I think.
There is no single answer to your question because it depends on so many factors. The basic pattern of these attacks is that the ship is held till a ransom is paid, so really it is a matter of trauma to the crew and delay to everyone else.
As between owners and charterers, it depends on the terms of the charter/s.
Some terminology. A “time charter” is one where the owner is paid by the day. A “voyage charter” is one where the owner is paid a lump sum for achieving a voyage. A “disponent owner” is the term for a charterer of a ship, when discussing them in their role as “owner” as regards a further sub-charter.
Generally, charter chains are chains of time charters, and it is only the final charter that is a voyage charter.
Time charter chains are almost always on “back to back” terms (but vary in only commercial terms ie daily hire rate, length of charter etc). In other words the wording of the charter is the same as between the actual owner and the first charterer, and between that first charterer (or “disponent owner”) down to the next charterer. This means that if an event happens then it has the same consequence right up or down the line of time charters.
This means that as regards piracy, it is usually either the owner at the top or the final time charterer who will bear the consequences.
There was a case last year where it was decided that certain time charterers had to continue paying the daily amount for the ship to owners while it was being held by pirates. However, only a slight and reasonably commonplace change to the charter terms would probably have had the opposite result.
The loser under a voyage charter if a ship is delayed by piracy is the owner (either actual or disponent), because the voyage charterer pays no more for the delay.