One would think so but I went and checked. In a Lost Vikings SNES ROM image, search for a sequence of VM opcodes. The turret program shown has a bit that goes 97 00 01 00 9C 18 08 2F 00, doesn't seem to contain any addresses and is long enough to not just appear at random. It shows up in the ROM image so it looks like yes, the VM was used in the SNES version too.