Have people really shifted from 2sf/mini2sf? I saw some of the early NCSF work (I think, I might be confusing another attempt I saw at another format for the DS) and was not impressed with what I saw. It seemed to be heading down some of the stranger paths for audio replication that I have seen in the hacking world, granted it was probably the easier route at the time than trying to bash the vio2sf plugins into using one of the newer desmume sound cores.
Anyway back on topic the sounds will not be the same as midi does not use the same sounds as people might have used on a given game on the DS. Some people did smash midi or some traditional sequencer setup and a sound bank (typically the DLS format, vgmtrans being able to convert sbnk into something resembling DLS -- it worked for some things but I had a hell of a time getting its output to work with openmpt where it worked fine with some other random non vgmtrans DLS files I downloaded elsewhere) and get it working with something like fl studio or awave studio (I recall seeing it in some of the guides on game specific hacking forums, possibly also pokemon hacking forums).
foobar and such should have the option to export as wave if you wanted full replication without having to hope your playback device can be coaxed into playing back s2f or whatever.
Oh and as you asked there are three main things I see that spit out midi from SSEQ
ndssndext that you have already seen
sseq2midi, a couple of versions out there including some newer stuff from loveemu
vgmtrans. loveemu decided to get the source and work on it a while back so you might have something nicer there now.