TLDR version, Most of Nightblood's initial investiture was from Ruin (but actually Harmony), rather than Endowment.
There's a few wob's that I'm looking at here. First, there's a wob that Nightblood started out with more investiture than 1000 breaths would account for, then there's a wob that Nightblood is connected to Ruin in some way. The third wob stated that Harmony had to do something with Ruin's extra investiture to keep it in balance with Preservation. The final wob related is that Nightblood has been to more worlds than Roshar and Nalthis.
So my theory is that Nightblood wasn't actually created on Nalthis, but on Scadrial. We know (from yet another wob) that Vasher and Shashara were worldhoppers before creating Nightblood, so it isn't impossible that they'd been to Scadrial. One reason they might have tried to make Nightblood on Scadrial is that they might have belived that (incorrectly) that the metal on Scadrial contained investiture. Harmony knew that he had too much of Ruin's investiture, and had to get rid of some, so helped invest nightblood (probably without them realizing) while it was being created. A possible reason for him to do this would be his shardic future sight.
The most popular cosmere timelines don't quite fit this theory, but I wasn't able to find any wob that actually ruled out my crazy theory.
Maybe I missed a wob somewhere, or a line in warbreaker that disproves my theory, or maybe I misunderstood something, but if I'm not, this theory accounts for the mystery of Nightblood's extra investiture, and Harmony's missing investiture.