I have done quite a few homes with just what you are describing. 3 choices here.
1. Replace shakes
2. Prime and paint shakes and live with the line just under the edge or lip of the shake.
3. Take a grinder and grind off the ridges and prime and paint to make for a smooth shake.I use a buffing grinder,with a #36 grit disk.It is adjustable with speeds and makes quick work of paint removal.Just be very careful to not make big cuts or lines in the shakes or they will appear in the final product.I will also hand sand any other imperfections in the shakes.It is a time consuming task and a lot of skill is needed,but it does make for a good paint job with out having the added expense of replacing ceder shakes. I used a good Oil base primer then applied latex for a top coat,No spraying. Use a brush for better penetration and build up.
Good Luck to you.