Kohen Kappa Coefficient of Naive Bayes with 62% overall accuracy is better than Logistic Regression with 98% accuracy?
Logistic Regression is only predicting one class (in this case the negative class)! Because of the high imbalance in the data, this model gives a high accuracy score. This metric, however, isn't reliable for imbalanced datasets. A more proper metric like Cohen's Kappa penalizes this behavior.

Naive Bayes, on the other hand, tries to predict both classes. It misses a lot more predictions this way, but it's Kappa is higher.