You've noticed a quirk of verb negation in Korean. There are many (6?) ways to negate verbs in Korean, depending on the sentence mood and how strongly you are negating the verb.
- 이 식당이 안 어두워요 = "This restaurant is not dark."
- 이 식당이 어둡지 않아요 = "This restaurant is not dark."
The short negation just places the adverb 안 before the verb. The long negation uses the verb auxiliary (for the declarative mood) ~지 않다 and conjugates the new verb.