Production boat builders usually use single conductor wires.  These wires are assembled off site into wire harnesses and laid into the boat at a stage of construction where access is most available, usually before the deck is attached.  By doing it this way boat builders are doing their best to automate the process.  Wire harnesses made up of single conductors are physically more compact, lighter and also less expensive.  So it makes total sense for boatbuilders to do it this way.

Compare that with the boat owner doing a rewiring project later in the life of the boat and you will quickly see why single conductor wires don't make as much sense for that application.  The wires have to be dragged through holes and conduits, often where they don't easily fit, and in the process they get subjected to a lot of abrasion and potential damage to the insulation.  Having an extra jacket is one way to minimize the potential damage to the insulation.  So in most cases it makes much more sense to use duplex or triplex wire for rewiring.  The only case where single conductor wires usually works out is areas with very confined access like ceiling voids.

There is one other point to consider:  The ABYC standards require for AC and DC wires to be bundled separately.  The outer sheathing of duplex and triplex wires counts as sheathing, so when using these wires you can run them in the same conduit.  If using single conductor wires then AC and DC wires have to be bundled separately.