Normally, the new ship is still called Enterprise. Checking my manuscript for Greater Than the Sum, I find that I only use "Enterprise-E" on three occasions in the text proper, two of which are meant to distinguish it from earlier ships of the same name (though I'll grant the third is gratuitous). The term "Enterprise-E" occurs only once in the current draft of Losing the Peace. I find it 14 times in the manuscript for Q & A, but 11 of those are in chapter headings, only 3 in the text proper. It occurs only once in the entire Destiny trilogy. I can't give exact figures for Resistance or Before Dishonor, since I don't have the manuscripts for those on my computer, but skimming through them by hand, I find plenty of references to the ship simply as Enterprise, and no usages of "Enterprise-E" turned up in my cursory search. Every location heading in BD, unlike Q & A, calls it simply "The Enterprise."
Well for me as a reader it doesn't make a difference if it was said in dialogue or in narrative. When used to distinguish it's of course usefull. Even to me
So the vast majority of the time, the ship is still just called Enterprise. And none of the "Enterprise-E" references I found were in spoken dialogue.
As I don't have any manuscript on my computer, I have to rely on what you say and more so what I have come to feel while brushing up on the latter Star Trek literature.
Well, the number of books you mentioned leaves the "A Time to..."-series as the source of my feelings.
One more thing: Could you do me a favour, while we're at it, Christopher?
I seem to recall at least the one time use of the term "E-E". Could you check that out for me via a script search please? Most likely it was in Resistance
so chances are, that you'd search in vain...