In LCMS, you will get much better sensitivity of Na-sugar adducts in the EICs compared to sugars themselves. The same principle will work for NH4 adducts as well, but there are notable drawbacks. The problems with NH4 is that it will change the pH of the mobile phase and its concentration is hard to control in the sample. 

Hence, given both strategies will work, there is no reason to choose NH4 over Na.