Welcome to the board ... it helps to know make, model, year, and mileage. he ECM monitors much on the bike. The black wire is the signal from the ECM that turns the alternator on. For example, when you start your bike, the ECM allows the alternator to begin to charge several seconds after start up.
Yes ... it can affect charging but look elseshere first. What are your symptoms? Have you checked the basics first ... battery connections tight and clean, has the battery been tested?
2002 with 102,000 Miles.Has new battery,Tried two alternators(rebuilts),No draw or shorts,Black/yellow wire has battery volage with key on,Battery voltage at alt. main wire.No short in black wire to ecm but shows 4.3 volts with key on.
Did you check every fuse? Just because a fuse says it's for something that shouldn't be related doesn't mean it won't affect the alternator too. I've had the problem on my 2002 with a fuse going out for something I thought was unrelated that caused my alternator to not charge. That was on my second alternator. My first one did really go bad at 116,000 miles. I'm still going strong on my second alternator and 2nd battery with 165,000 miles.
According to other Honda alternators, the black wire's terminal sends out a pulse width modulated signal that the ECM uses to determine if the idle speed needs to be increased due to excessive load at idle. If I'm understaning you right, the battery voltage is 4.3 with it running? If so, you may have something else wrong in the path between the battery and the alternator.