Yes, all the same formats are supported via USB. So, 24-bit/96kHz FLAC can be played back via USB for example.
However, please note the following;
USB is absolutely not the best way to use the NP30 the USB connections are merely there for convenience to let you connect a memory stick, etc with some tracks on it.
The intended functionality of the CXN / 851N / Stream Magic 6 / Minx Xi / NP30 is as a network player using UPnP.
When browsing a USB HDD, you are simply browsing the file/folder structure. So, if you haven't alphabetised/categorised your music it makes it almost impossible to navigate.
For example, if you had 1000 random tracks dumped in no particular order on a USB drive, there would be no way that you could navigate by artist/album/etc...
However, UPnP uses the metadata contained within a track/file to browse. This means that you can now browse the same random 1000 tracks by artist/album/genre/etc because the CXN / 851N / Stream Magic / Minx Xi / NP30 looks at the metadata within each track, rather than just looking at the individual file name.
Of course, using the metadata also gives you added bonuses such as album art if using the app.