There was a thread on this a short time ago. A single, large propeller turning slowly gives more thrust (speed) while smaller, faster props give you more precise control in close maneuvers.
Multiple thrusters can act as a back-up system if one fails.
It would seem logical that a combination of the two would be best.
It depends on what purpose your sub is designed for.
If you want to motor over a long distance, moving quickly, a large propeller and a sleek torpedo shaped hull is best.
On the other hand, if you can tow, carry, or otherwise transport your sub to the dive site, and want to see something close-up, work, photograph, salvage, etc. then small multiple thrusters will be needed for the fine adjustments needed for that.
If, for instance, you want to attach a cable to a sunken boat, or move vertically along a wall to photograph the life, or anything that requires precise control, a single large prop wouldn't work at all.
I'm building my sub with two thrusters in the back with a rudder/dive plane mechanism for main forward/reverse propulsion.
Additionally, the two reversible side mounted thrusters can pivot 90 degrees from horizontal to vertical so up/down, forward/reverse, left/right, or spin without moving can be done.
With all four in the forward position, at full speed, the total thrust is 400+ pounds.
A little extra thrust might come in handy when I need to push against a current or push the sub to the surface.
Some of the main things to consider would include: purpose, complexity, cost, reliability, replacement/maintenance, power consumption, and maybe entanglement.
I'll be watching for answers from the other guys on this to see what else is important.
Frank D.