Once you kill an enemy, it will stay dead and won't respawn.
Patches for both (U) and (J) versions.
Ninja Gaiden II - The Dark Sword of Chaos (U) [!].nes
CRC32: 9D135A8E
MD5: 2B9570720145F760AEF1EF04814ABE92
SHA-1: B1796660E4A4CEFC72181D4BF4F97999BC048A77
Ninja Ryukenden II - Ankoku no Jashin Ken (J) [!].nes
CRC32: 516BA002
MD5: F255F44D47EE64D6B040B1AFEA50165C
SHA-1: AE1BD1563C31EBE54078F8876ADDFB30D905D0A4