In the 16 years we've owned our twin engine boat we've not found the operating cost to be much higher--- or in some cases any higher--- than the costs acquaintences have with single engine boats. For the most part, you buy twice as much lube oil and two times the number of oil and fuel filters. Compared to the overall cost of owning a boat, lube oil and filters are free.
Fuel burn is not twice that of a single, assuming the same type of engine in the same type of boat. We run our two engines at 1650 rpm to get 8 knots. People we know with the single engine version of the same boat we have run their engine at 2,000 rpm to get 8 knots. And their one engine is working harder than each of our two engines. So as near as rough calculations can figure, we burn perhaps 1.5 times as much fuel as the single-engine owners (of the same boat). In the overall cost of owning a boat, that difference is irrelevant.
While we have occasionally had to replace ancilliary components on our engines--- oil and transmission heat exchangers, the water pump belt, a pinholed fuel injection pipe--- these never occurred at the same time on both engines. So compared to the overall cost of owning a boat, the occasional additional parts required were an insignificant cost.
There were three times when having two engines resulted in a cost that was significantly higher than if we'd had just one. One was when we had the exhaust systems that were on the boat when we bought it replaced with new, custom-made fiberglass systems. One was when we had the motor mounts on both engines replaced, a once-every-thirty-years-expense, and once was when we had both raw water pumps replaced with new, one-piece pumps (we went ahead and changed both engines even though only one actually had a problem with its pump drive coupler).
So while it's true that over time, two engines will cost more than one in terms of maintenance and repair, this extra cost will be spread out over so many years that it is insignificant.
And.... our "spare" engine under the floor has prevented us from having to come home on the end of a very expensive rope four times. What we didn't have to spend on tows--- a couple of which would have been very long ones and extemely inconvenient--- probably more than made up for whatever running two engines vs one costs us.
And.... we have friends with single engine boats who have had to spend far more repairing their single-engine setup, plus towing costs, than we have spent on our two engines.
So based on our 16 years of experience with a twin-engine boat, we don't buy the "costs twice as much" theory at all. It certainly CAN cost twice as much depending on the condition of the engines and drive trains and how the boat is operated and maintained. But it's not an automatic given.