In fact you use an accusative in those greetings. (You can imagine that the sentence begins "I wish you XXX- in accusative.)
And because noc (night) is feminine you have to decline the adjective like a feminine too. So you get dobrou noc..
Den and večer (evening) are masculine and there nominative and accusative look same. .
Ráno (morning) is neuter so you get Dobré ráno.