Well, normally, I'd agree with you. But StableBit Scanner isn't tracking the scan as one whole thing. It actually uses a sector map of the drive. So it tracks sections of the drive, independently. Each section is checked based on that status, and it over time, spreads out when the scanning happens. And should actually make it more intelligently scan (by ideally scanning at times and days when the drives are less likely to be active).
You can check out this by double clicking on the disk, and looking at the sector map. It will show different colors for different regions.