If you're talking seamless branching between the new and old visual effects (as is done on the TOS DVDs) then the cost would be minimal. But if you're talking about including the episodes in their entirety in both SD and HD, that's going to use up much more disc space, and result in more discs per set. And that's going to substantially increase the cost.
Bullshit. Blu-ray discs have FAR more storage space than a DVD. You can easily add SD episodes on there alongside the HD ones without needing to add more discs.