I don't think that the case remnant n has anything to do with the fact that goedenavond etc. are written in one word. The n could remain there for the fact of simple pronunciation: in goede(n)morgen one can't hear it at all, this in contrast with goedenavond, where it is clearly pronounced between the two vowels. The greetings goedemorgen (I would write this without an n!), goedemiddag etc. are very common words, used every day by thousands of people. They are considered just a word of greeting, not a real wishing sentence like 'I'm wishing you a good day.' Therefore they are written in one word.
Other expressions with case remnants (like te elfder ure 'at the eleventh hour' or de heer des huizes 'the master of the house') are formal and almost completely restricted to written language.