Are you using the Digital Waveform Editor v1.0.x? If you are, then that version of the editor only supports writting to DWDT and U32 file formats. Hence reading those files as U16 has a conversion overhead that will slow your application down.
The Digital Waveform Editor v2.0 has support for writting both U8 and U16 HWS files.
To see if this is the issue, let's use a LV VI to re-save your HWS file with U16 data. Then benchmark your application again using the newly created HWS file. I've included VIs to convert your DWDT or U32 HWS files to a U16 HWS file (they don't overwrite your existing files, they just create new ones).
Reply with the results. If this doesn't help, we can look into something else.
-Jared