Did about 4 heads this past summer on both my old engine and a few friends. Those blocked holes are generally superficial blockages, meaning they don't extend far. What I did was use a shop vacc (running) and positioned right over each hole as I disturbed the grud with a screw driver. You will note it will suck right out of there and you will also see it is only about one quarter to a half inch deep. Of course also check the head (which you did) Have a good look for cracks in the block there, like weak or thinned out areas. I've found that if it's brownish it's usually gunk building up because (of what I think) is heat. I've noticed it on cyl 1 and 2 on engines that slant rearward with the No 1 cyl forward and high. Not real sure of the correlation. Have seen black as well which I thought was a build up of carbon from an exhaust port crack leaking into the water jacket area or perhaps around manifold studs etc.
What you were looking at is the reason I do muriatic acid flushes of my engine every 2 to 3 years. When I took the head of mine, nothing of the sort was there but the other 3 sure did. So clean them out the best you can, see if you can blow compressed air through after, then reinstall the head. Once you run up the engine, check or leaks on your hoses etc. Once convinced there are no leaks I'd do a muriatic acid flush and continue to do one every couple to 3 years. I'll post Mr. Don Moyer's link beneath.
Hope that helps and perhaps others have an even better idea of how to deal with it.
https://www.moyermarineforum.com/for...20the%20engine).