I'm using it without any issues, atmosphere 0.17.1, installing from USB hdd formatted with ntfs fs works perfectly here. This application is the best installer all around for its simplicity while maintaining the nca verification process and now this awesome hdd support.
EDIT: Only issue I found till this moment is that it doesn't check for the available free space before installing. If trying to install something larger than the available free space, Atmosphere crashes without warning. But I guess the same behavior also happens on tinfoil / lithium from what I remember. Couldn't care less for sounds and themeing like other people are nagging about, the simpler the better.