It would be great to see a side-by-side test of this. Here are few things I have noted about singles vs. twins with the same combined horsepower.
Fuel economy drops by about 30% with twins due to the extra drag from the drive, and the extra weight.
Cost is often about the same. It seems Mercruiser, Volvo, and others almost price by the horsepower. Now a Merc 1350 is probably a different story, since that pricing is stratospheric. If you price two small blocks with one big block of equal power, they come out about the same.
Weight is an issue. Twins definitely increase the weight. This could change some in the future with the new all aluminum GM small blocks.
Twins are up to twice the maintenance, and is usually twice as much to go wrong. The lower horsepower engines generally have somewhat less expensive parts though, and sometime less maintenance is required. Twins are usually less highly stressed, so they may last longer.
Engine access for maintenance can be a pain with twins, since they are usually put right next to each other with very little clearance.
Top speed is generally lower with twins vs. a single with the same combined power. Again, more weight and drag play a factor.
If you do much boating out in the ocean or Great Lakes, twins are pretty much a must. The ocean doesn't take prisoners. Even just leaving the harbor is a risk in a single. I've had engines die right in the harbor. If the engine dies right outside the breakwater, the boat is going to get slammed on the breakwater rocks by wind and swells, or get thrown onto the beach. Trying to pay out 300 feet of anchor line is pretty much impossible that close to shore or breakwater.
If you go any distance from the harbor, help can take a long time, and it may be too late to save the boat from grounding or being swamped. If you cross shipping lanes, and your one engine dies, you can be in trouble. The ships may not see you, or may not be able to turn in time. If you run along the shore, and your one engine dies, your boat can be on shore in a matter of minutes. I had to shut the engine in a single engine boat one time off the SoCal coast, and with the wind and waves pushing the boat, my GPS said I was going 4 knots backwards!
I saw a story on these forums about a guy in a Schiada racing along the SoCal coast in the Rum Run. He blew his engine. He threw out two anchors, but they wouldn't hold because the swell was too big. He radioed race support, but it was going to take at least 15-20 minutes to get there. It was clear the boat would be history by that time. He was getting ready to abandon ship using his raft since the boat was approaching the breakers, when another competitor came by, and dragged him further from shore so there would be time for support boat to get there. The competitor then went on his way. Talk about sportsmanship! You can see the thread here
http://www.performanceboats.com/jet-boats/92680-72-tahitian-22-jet-boat.html
Michael