watching South Main Auto and Pine Hollow Auto Diagnostics, often the problem with modern electrical/electronic systems is bad ground and broken wires. The scanner can't tell you that directly, it can show communication faults etc.
So the issue is that the technician has to know how the sub-system is supposed to work and follow the flow of current to figure out where the problem is. All Data seems to help a lot with that but it's too expensive for most DIY guys to justify.
This kind of work involves looking at connectors, looking for green corrosion on terminals, looking at wiring harnesses for chafe marks where it has rubbed against a sharp edge and shorted out a wire, etc.
I had an intermittent downstream O2 sensor code (P013, IIRC) and thought I had to replace the original (27 year old) downstream sensor on my 98 Jeep. Turned out it was simply oxidized terminals on the O2 sensor connector, a little contact cleaner and compressed air and no more code.
A few years before that, I had a lazy O2 sensor, this one never set a code but you could see it if you looked at the live data stream. That one required replacing the sensor to cure the performance problem caused by the lazy sensor (which caused the EFI system to over-correct).
Sometimes you can use hot functions to "fix" fault codes. Example, I had an intermittent ABS light on the same 98 Jeep, it would come and go with no rhyme or reason. The code suggested the ABS control unit wasn't passing the start up self test. So just on a hunch I used the hot functions of the Autel scanner to actuate the ABS pump, after that, no more light. My guess, a slightly sticky old ABS unit.
The reasons why I say I am not a fan of CANBUS systems for those who keep their cars a long time and live in a damp climate:
1)corrosion/oxidation, there are many more points of failure, than with old style DC wiring. If you live in a dry climate out west it is totally different here. Bad grounds, connectors with green corrosion, etc.
2) Complexity: take a look at Painless Wiring's brand-new full wiring harnesses for classic cars and Jeeps vs what's in modern cars. There is no comparison in the number of connectors and the complexity of the systems used.
3) parts availability, after 10 years good luck finding new replacement modules and ECMs. The become NLA and you're left with junkyard parts. Sometimes they work sometimes they don't.
So in my opinion with boats especially you're better off with a Mercrusier powered boat with a carb. Modules? Just for the Thunderbolt electronic ignition unless it's even older and has points. Points are easy to change, and to adjust just ground the coil lead, crank it over with a remote starter switch and use your dwell meter to get an accurate setting. Easy. Even on my OMC where many parts are NLA, the only module is for the ESA, and CDI electronics still makes them for both points and electronic ignitions. 
Carb rebuild kits are available anywhere, even if a carb has internal corrosion, they can be replaced with a brand-new Holley or Edelbrock either of which is fully supported for parts. Unlike the OEMs habit of making things NLA. Thanks to the classic car aftermarket, I can get any part I need for a Quadrajet carb that hasn't been made in over 30 years. Mechanical fuel pumps, (Carter the OEM manufacturer) can be bought for like $75. Low pressure electric pumps for carb engines are not much more.