Odds are an NPC you are creating for a supplement uses rules for the supplement that (unless you are the programmer of the tool) can't be supported before you release the supplement.
For (potential) publication? By hand, or both (to compare results). Somehow I don't trust those programs that much... but it's always good to double-check.
Only if the NPC is for my homebrew and the stats aren't that important I'll use a program...