The only reason you can see the cracks is because the shadow of the crack is darker than the surface of the wood. If you coat the hull first, you will fill the cracks with clear epoxy and actually that's all you can do because there won't be any cavity to fill but it will still be dark. If you first fill the larger ones that really stick out and bother you with a mixture like the wood surface then you won't see them.

Be cautious because of two things: the wet out wood gets darker and the putty mixture hardens a bit lighter. So mix your putty to pretty much match the wet wood.

HOWEVER. When and if you fill them, you will contaminate the surface next to the crack unless you mask. So make sure you sand the area thoroughly and wet it with water before epoxying to make sure it's not contaminated. If the filler is there, It will really stick out and look way worse than a crack.

My opinion is only bother to fill anything that is pretty big.

Actually, want to do it right? Take a piece of strip, cardboard thin, and plane it to a knife edge. Break off pieces and tap them into the spaces with a little glue. Once hard, shave them flat. You will never see the cracks or a color difference.