I've had Windows and Linux (Gentoo) installed on separate hard drives, and there was no problem, as long as Windows is on the primary hard drive. Or at least, the Windows installer will refuse to install onto any drive other than the primary one (or on to any partition other than the first), although I think you might be able to swap the drives after installation and thereby get Windows on the secondary drive. But I digress.
Anyway, the point is, it certainly should be possible to install the two OS's on separate drives, but it's not necessary. You can, if you like, divide one drive into partitions and install Windows on one partition and Linux on another. (That's what I do) Some distributions' installers will handle this for you, I'm not sure if Mint is one of them. If you do this, you can use your second drive for data only. You'd probably want to format it as NTFS because that's reliably readable/writable from both Linux and Windows.
As far as whether it's a good idea: to get the fastest disk access times (and to prolong the longevity of the drives), it's probably best to split the workload between the two drives. Since you're dual-booting, you'll only be using the system files of one OS at a time, so it makes sense to put both operating systems on the same drive and a data partition on the other. That way, no matter which OS you're running, you'll be making use of both drives. The alternative, putting Windows (along with a smaller data partition) on one drive, and Linux (along with another data partition) on the other drive, is likely to stress out one drive more than the other, depending on which OS you boot into - unless you're careful about how you distribute your data files between the two drives (but who wants to do that?).
