Well the NPCs list (which includes
all uniques, not just major NPCs anymore) only includes those destroyed by you or your allies. It's meant as a tally of your kills under the combat section, not a record of who was killed.
(Specifically the scoring part was because that's not handled in code, but by specific scripts written for some of the NPCs, which aren't usually able to be on a different faction so I hadn't thought to do any faction check there, though obviously those are a special case since there are ways to control them
)