One is your raw water
intake for the engine
. Inside the boat you will see a seacock attached to it. Make sure the whole thing is sound and clean. Exercise the seacock temporarily. If you are ever to turn the engine without starting for many tries, close this intake or else you may flood the engine.
The other is a ground for some equipment
or else a radiator for a fridge (but I bet it is a ground. It should never be (have been) painted over in the first place. You may try to clean it but it looks like replacing will be more productive (if you do need the thing in the first place).
The rubber boot is OK and a typical Volvo Penta
gland. While on dry undo it, clean and grease with VP gland grease. If absent, use vaseline. Make sure it is sound and has no cracks, etc.. VP recommends changing these every X years. Once in water you will squeeze it slightly to let some water in and air out. If afterwards it drips too much, turning it slightly every 15 degrees or so normally brings it top a perfectly dry position.