Configuring a date picker with support for disabled dates
You don't need to build the options object in one go instead create what all cases need and then optionally add:

options = {
    firstDay: 1,
    dateFormat: "dd.mm.yy",
    altField: '#reservation_dates_input',
};

if (disabled_dates.length&gt;2) {
    options.addDisabledDates = disabled_dates_array;
}
if (reservation_dates_input.length&gt;2) {
    options.addDates = reserved_dates_array;
}


you also have some code duplication when creating the arrays, you can put that in a function and call it twice:

function createArrayFromInput(dates_input){
    if (dates_input.length) {
        var clean_dates = dates_input.replace(/\"/g, '');
        return clean_dates.split(", ");
    }
    return [];
}