You should provide a reproducible example to set the context. Sometimes, answers aren’t readily available unless we try. Also, you should specify which programming language are you using.
naiveBayes is a multiclassification algorithm. There would be no problem in using a variable with 41 levels. However, naiveBayes isn’t the best algorithm to impute missing values. The reason being, it makes “naive” assumptions of independence and importance in the data set, which aren’t always true. This parametric nature makes it less powerful than tree methods.
Instead, for missing value imputation, you should use a tree based method which is a lot more robust to missing values. If you are using R, you can get reference from here: https://www.analyticsvidhya.com/blog/2016/03/tutorial-powerful-packages-imputing-missing-values/