Bluey Hi,
I would say that it is definitely worth investigating. The black flecks could be either rubber material from a seal, or possibly more likely carbon. If carbon, they should crush to a powder.
That aside, you appear to have a definite coolant leak in the top end, and this needs to be looked at. If you do this , have a really good look at where the cylinder seals contact the head. A small amount of corrosion/pitting here will promote leaking. Rotax allows you to skim the head up to 0.012". Obviously this should be recorded in the engine logbook.
Also worth considering is that even a full overhaul only replaces most of the consumable items and not all. The rest of the engine will continue to wear/deteriorate, and you seem to have a lot of hrs on this engine. It might be worth you considering replacing with a new one. Expensive, I know, but it really does give you peace of mind. Hope this helps.
Safe flying
Kev