There's not good software to do this nowadays, and there certainly won't have been then.
The pictures were hand-drawn first, but they would have been converted to pixel art by hand - pixel by pixel. You could do a similar thing on any art program - just resize your image then trace over it on a new layer.
Look at Anri's official art and then her pixel portrait: http://shining.wikia.com/wiki/Anri
You can see that they clearly used the hand-drawn art for reference. This is the same for all the characters