There are other reasons, such as wanting more HP (some have gone to the Merc. 115 or the Suzuki 115, both of which have bigger blocks) For me, if I keep the 22, is the alternator output, and carburetor engine. The 2006 on down on the 90' only put out 17 amps (and some is used for the engine, the instruments, and not a lot for charging the batteries.)
The current Honda 90's are injected, they put out 44 amps, with 35 amps available for battery charging.
It does not pay to just change an engine for minor issues--and many run well into the thousands of hours. The ones which run the longest are in commercial use--such as marine patrol, coastguard, charter boats and tow boats. They are run every day--much of the time at low RPM. They are also maintained well. Some of these are seeing over 8,000 hours of use.
Also look at corrosion. I looked at a 2005 boat yesterday, with 141 hours on the tach--There was no engine computer readout to verify that. But the lower unit had the corrosion painted over. It was significant--enough that it raised flags for me. (This was a Honda--and I have noted that the Honda's tend to get some corrosion if left in salt water for periods of time. I was told that this boat was rarely left in the water, and was stored on the trailer 99% of the time--again the corrosion seen tends to belie that...
If I look at a boat with 1950 hours, I am discounting the price to pay for a repower. The 90 Hondas are going to run in the $10,000 as a very low number on up to as much as $15,000. I have a friend who just had a repower of a Suzuki 150 (from a Honda--low hours, be corrosion had eaten up the water passages). He paid about $15,000 all up for re-rigging, gauges and controls.
On the other hand, I take my boats out of the water, they are run in fresh water for the last 15 minutes going to my boat lift, and there is minimal if any corrosion on my 2006 Honda... with about 450 hours--no reason to repower.