I have the same thing on mine! I'd tried to scrub it off and when that didn't seem to be effective I assumed it was some kind of wear that had worn off the gelcoat off the bumps. I had resigned myself to a coat of deck paint!
Your note prompted a closer look. Most of it is, as you suggest, a kind of algae and can be poked out with a pin. Tedious! An old toothbrush doesn't touch it. If you give it a good soak first, a brand new toothbrush does winkle it out. It will still take a while to do the whole deck but it beats a pin. Maybe there's a bigger brush that has thin stiff pointy bristles like a new toothbrush.
Then there's another type of blackdots. These seem to be little round holes in the tops of the bumps which must be a defect in the first layer of gelcoat that went onto the mould. I can't think of a way of getting them to be less conspicuous. They are luckily much rarer than the algae spots and on my boat only in one place (deck between the mast and the hatch)
Geoff Cygnus P21/30