Yes, probably that is the reason that Windows has enabled both services. What SSD do you have and how big is it? Since a a lot of the Superfetch/Prefetch data are going to be stored in that SSD, it doesn't have any effect on files stored on the SSD but on the other hand it may speed up other software that gets loaded from other HDDs. However that also depends on the specific software and your system since there have been users with HDDs that said that they saw a noticeable increase in system responsiveness after disabling SuperFetch/Prefetch. Also there are reports that those services speed applications but have no effect on games. Finally keep in mind that the RAM amount of your system also plays a big roll since it's being used for caching some of that data.
As you can see there is no definite answer whether you should disable them or not and it also depends on your system configuration (SSD, RAM, HDDs). If you have an SSD it is always recommended to disable them in order to avoid unnecessary writes on the SSD. However in your case and since you have 2 HDDs with software installed you could disable them and monitor the system behaviour. If you feel your system is getting slower re-enable them. Finally keep in mind that the SuperFetch/Prefetch are considered obsolete in today's modern SSD PC systems and most users disable them if they aren't disabled by the OS (Windows) automatically when it detects an SSD during the OS installation procedure.
For more info check this => https://helpdeskgeek.com/help-desk/delete-disable-windows-prefetch/
Good luck.