My level of expertise in this area could be thin, but it would seem to me the only sort of problem one might encounter arises from to different boot-system Windows HDDs connected at the same time.
The problem would only occur if they have the same drive "signature." But unless one cloned an OS disk and kept the original signature on the second drive, there shouldn't be a any problem.
As for disks solely used for data, I don't think there are even any caveats, unless the data drive has a partition and format unsupported by the OS.