I have a question about the difference between the O scale files/disks and the smaller scale ones. Do the O scale models have finer detail (if reduced to my scale HO) than the smaller scale models, or are the sheets just arranged more effeciently for printing in the smaller scales?

Ron, The resolution is the same between scales. All Kits are created in O scale or larger and then reduced to the proper dimensions. The DPI is constant at 300 in PDF format. Some newer kits will be released at 600 DPI in future for those who wish to blow them up to G scale.
All kits are available in O and HO. Most kits are available in S and N from the web site (but not on disk).
Scaling from O to HO is very easy but you are correct the HO are layed out for better printing economy.

Thom