I had discounted 485 before, as I inherited a system with it that had many problems.
485 problems are (almost) always due to improper termination, you need the 3 resistor termination in one end and a one or 3 resistor termination in the other.
Can I get away with a bus that runs down the center of the ship that is tapped into by the nodes?
That will depend on the speed you want (note, with 9600 baud and 16 nodes, you only have abt 500 as effective speed) more below.
Do I need to be concerned with any effects from the cable and or connectors? What kind of speed can I expect?
Connectors are usually not that much of a problem as long as you make a and b neighbor pins. The cable should be routed so that you have very short stubs. The better you lay out your cable (short stubs etc) the higher speed you can acquire.
Would I use the serial port with a 485 driver? How many nodes have you used?
If you do not use a regular 485 driver (or a circuit EXACTLY following the 485 standard) you will not have 485, you will have problems. I have used as much as 51 ports. If you plan a lot of ports, make sure you use 1/2 load or 1/4 load 485 transcievers.

Read up on thNS appnotes, the link is in links <---- as "best app..." in the intersting sites sction.

Erik

Ps that seems a lot of effort to build a ship you are going to sink :-)

Erik