The huge difference in the quality between 16KHz and 48KHz voice using SLT is due to the 48KHz dataset itself. The 48KHz sound provide more spectral information and thus require more features and model parameters. There is no point of upsampling 16KHz to 48KHz unless you can retreive the spectrum between 8000Hz and 24000Hz.
You can use the 16KHz demo or reconfigure the HTS2.2 demo using your configurations.
I was trying to build HTS voice using version 2.2. But, my recordings are in 16KHz and HTS 2.2 seems customized for 48KHz samples. When I upsample the 16KHz files to 48KHz using SOX, frequencies are scaled to only 8KHz. How to upsample the recordings to 48KHz.
PS: I perceived huge difference in the quality between 16KHz and 48KHz voice using SLT.