Short-term this will cause a lot of inconsistencies with applications using low-level APIs as the files currently existing will be NFD normalised, but any user-given path will very likely be more or less equivalent to what NFC would do.
So in the short term, this will be a mess (unless the APFS conversion on install-time also does a once-time conversion of the normal form), but in the long term, I believe this is the way to go.
And for that matter, the same should happen with regards to case-insensitivity which is even worse as ensuring case-insensitivity might actually be dependent on locale, which means that depending on the user's locale two file names might or might not be identical under case-insensitivity rules.
Unfortunately, it look like there's just too much legacy code around that plain doesn't work with a case-sensitive file-system on the mac (I'm looking at you, Adobe).
BTW: On my 10.13 Beta 1 setup with an APFS converted boot drive, unless I manually create a NFD encoded file name on the command line (which you can't do accidentally), everything is NFC both in the UI and on the command line. This also applies to files I haven't touched since the conversion to APFS.