First thing I would check would be the air filter is clean, I've also come across a boat whose air filter pipe from the filter to the intake was rubber, when the engine was opened up the rubber laminate in the hose collapsed and restricted the air flow causing it to black smoke and lose power.
it's just a process of logical elimination.
Some diesels which are continually run at low revs, especially turbo's, don't necessarily run hot enough for complete combustion and tend to smoke a little, this smoke has a greasy/oily texture and as the engine is not running hot enough to eject it all some of it some tends to stick on the turbine blades and inside the exhaust pipe. A good hard run will get the engine up to it's correct temperature and burn off these deposits resulting in black smoke at WOT.
This will gradually diminish after 30 minutes or so.
If it doesn't then deeper investigation is necessary.
I've seen two stroke diesels used so badly that they could only develop around 60% of power output, the solution was to make a fuel mix of 50/50 paraffin/diesel then take the motor to WOT for up to an hour, ease back to 3/4 throttle for 5 minutes, then another 30 minutes blast at WOT until she's running sweet again.
The fuel mix burns hotter than straight diesel and burns off those oily black deposits, BUT do it away from everyone else as the resultant black smoke isn't pretty.
The alternative would be a complete strip down and clean of the exhaust system from the manifold out.