The difference is that in Nil rated items, the rate is 0%. Hence tax is 0. In exempted items, there is no rate of tax due to exemption notification. Basically the net result is the same in layman terms.
Unbranded wheat is Nil rated, branded wheat is 5%.
Wheat ( other than those put up in unit container and bearing a registered brand name ) is exempt supply .Vide notification no 2/2017 CT rate 28/6/2017 . Exempt or Nil rated supply means certain Goods or services are kept Nil rated or exempted in the public Interest , by way of Notification by the GOVT on the recommendation of the GST council .