The main difference between HDToolBox in OS 3.9 and HDToolBox in 3.2 is that they are written by entirely different people.
For OS 3.9, Joan Dow did a deep dive and created a new Reaction based HDToolBox and hdwrench.library pretty much from scratch, from what I understand. This HDToolBox supports ASKDEVICE tooltype which lets you pick which device it will use to scan for devices.
For OS 3.1.4 (and 3.2), the sources to Joan Dow's HDToolBox and hdwrench.library was not available and they (Olsen, I presume) went back to the sources of the 3.1 version, partly updating it to similar levels of the OS 3.9 one. But not quite, and certainly not without bugs.
So yes - keeping OS 3.9 HDToolBox and hdwrench.library (and resource.library) can be wise - especially if you have hardware that is slightly different than what's "mainstream".
And avoid HDInstTools.
