The black oil has something to do with the additive yamaha uses. The shearing of the oil causes it to become black. Wspitler, your assumption is likely true.
Where's Doc Stressor? He likely could give us the best answer.
I was up on Vancouver Island all week and had no cell phone or WiFi access. That was nice!
I have never drained a dual powered boat without noticing that the lube from lower unit with the counter-rotating prop was always darker. The dark color is the result of a higher amount of oil oxidation, which occurs at a higher rate with increasing temperature. It might have something to do with a sharper hypoid gear angle in the CR lower unit. Gear oil always darkens to some degree with usage. How much is too much? You would have to get the lube analyzed to know for sure. But 100 hr does not seem to be too long. Synthetic gear lubes tend to stay lighter in color because the base oil is more oxidation resistant than conventional stock.
The color of virgin gear oil depends on the additive package. Molybdenum anti-wear additives give a dark color.
You generally want to use a GL4 rated lube in Yamaha lower units except for the high performance models. They contain soft metal bushings that can be corroded by the anti-wear and extreme pressure additives in GL5 lubes. This is a slow process and some synthetic GL5 lubes claim to have inhibitors that protect soft metals. So little harm is done by using GL5 lube for a while. It's always best to use what the manufacturer recommends, however.
I've had a few water pumps fail over my 60+ years of boating. Interestingly, they were always on engines that were only used infrequently. What happens is that the plasticizer in the synthetic rubber impeller blades doesn't get re-distributed without use and the blades become brittle. I lost a blade on the 40 hp Suzuki on my skiff after only one year. I change the impellor on the skiff (which sucks a lot of sand) annually and on the Grady (only used offshore) every 2 years. I inspect the plate and housing and change them if there is any indication of abrasive wear.
It's a good idea to drop those lower units every year as folks are suggesting. If you don't, things can seize up bad. I remember taking a month to get the lower unit off of a 135 hp Johnson on my old 204C. The boat was only used during the summers up north and stored dry over the winter. So I figured that I could go for a long time without checking the water pump. After bringing the boat down to Florida, I tried to take a look at the impellor. The process took hammers, pullers, and finally a torch to remove that lower unit.