새 in this case is just a prefix for colors; 새파란 = vivid/clear/pure blue

어둡다 means "dark in the sense of having very little or no light, (figuratively) not easy to recognize" e.g. 어두운 방 dark room 어두운 하늘 dark sky (due to dark clouds) 밖은 벌써 어두워졌다 It was already dark outside. 귀가 어둡다 be hard[dull] of hearing 눈이 어둡다 be weak in (eye)sight 새 means "dark in the sense of approaching black in hue, deep" e.g. 새파란 하늘 the deep-blue sky, clear blue stky