The rationale for having both is unclear, but for reference, WM_NAME is of ICCCM encoding (meaning it's one of six thousand possible encodings, specified by the TYPE atom), while _NET_WM_NAME is guaranteed to be UTF8, which is just a lot simpler. So, consider WM_NAME deprecated, and _NET_WM_NAME the replacement.
We might just want to fix the wm spec as Thomas suggests, rewording it to "If set, the Window Manager MUST use this in preference to WM_NAME"