I didn’t watch Ninja Scroll when it first came out, which is good, as I was a little young for the subplot of Kagero’s body is so filled with poisons that her kiss can kill a man, but I do remember the multiple ads plastered through the Marvel comics of the day (it was the Age of Apocalypse-era!). As for who did watch it, well, that includes the Wachowskis, who adopted the visual style of the film for The Matrix, which you can see in the flowing trenchcoats and bullet-ballet of the famous lobby shootout.
The siblings were so impressed by Ninja Scroll that they brought on its creator and director, Yoshiaki Kawajiri, for The Animatrix, the anime collection of shorts that takes place between the first and second movies. Kawajiri wrote and directed The Program short for the collection.