I'd also go for logistic regression since you don't mention that you have a time variable specifying the time from inclusion in the study until start of smoking or censoring (end of study); in that case a Cox regression would be better.
I doubt that there is any difference in using percentages as predictors as compared to other continuous variables. For example, BMI (Body mass Index) is neither a directly measured predictors, as it is derived from a division of two units.
As Glen_b mentions, these predictors might not be truly linearly associated with the dependent variable. But transforming them might make predictors more difficult to interpret and journals typically don't like transformed variables if they are the predictors of main interest.