For models needing displacement, 6 or 12v gel cells make a good choice for adding ballast, but you can also gang up multiple 7.2/8.4/9.6 v rechargeable packs if you like, for higher amp-hour capacity.
For gel cells, 12v offers more flexibility- more accessories (like water pumps) are available that run on 12v. And a motor sized correctly for a 12v system will draw fewer amps to deliver the same power than a motor sized for the same power on a 6v system… not a real issue, as the wiring isn't really a problem in either case.
You want to get all your accessories together and check that either voltage is ok. For example, Graupner's bow thruster comes with a 7.2v motor that will run ok on 6v, but 12v is too much- you'd need to swap motors, or use it with an ESC and limit the max throttle (possibly with EPA adjustment on your radio). And many ESC's are ok with 7.2-8.4 v, but not 6 or 12 (Mtroniks is a good choice for 6 and 12v marine usage).

Harbor Models offers a power center which takes 12v and gives you regulated 6v outputs, if that's better for some accessories or lighting.

Patrick Matthews