I found a solution to this problem.
Ninja form fields are being loaded dynamically after the whole DOM is set up so when you are using
jQuery("#nf-field-X").attr("placeholder", "your custom placeholder text goes here");
the datepicker don’t even exists.
To tackle this use this code
jQuery(window).load(function(){
jQuery("#nf-field-X + input").attr("placeholder", "your custom placeholder text goes here");
});
which will be executed after all the ninja form fields are created.