So, you have Windows software. This "Windows 9x Subsystem for Linux" just boots Windows 95. I don't know what you would use the Linux part for. Care to explain more what you want to do?

If you want to run your windows software in Linux, you could try Wine. Wine seems to have support for WNASPI so it's possible your software would just work. (You might have to run Wine as root I guess, to get access to the SCSI devices.)

If Wine doesn't work, Windows in QEMU with PCI passthrough to the SCSI controller might have better chances to work.