I suppose it would depend on the puzzle, but let's use a standard 57mm 3x3 as an example:

Do you think it would be cheaper (in material and labor) to upload just unique pieces to Shapeways, order those, then make molds out of them and repeat the casting process until you have the required number of pieces?

OR

Do you think it would be cheaper (in material and labor) to upload the entire puzzle to Shapeways, order the puzzle, then make a gigantic mold with all pieces, having to only cast piece once?

The reason is that I'd like to sell puzzle creations in the future, assuming selling hand-casted puzzles would be cheaper than just having customers purchase from Shapeways.

Almost always Shapeways is cheaper but casted puzzles can be worth more. What types of puzzles are you wanting to make?

I currently have a mini 5x5 on paper, that to my knowledge doesn't infringe on any protected designs; as well as a tall mirror 1x3x3 (technically bandaged mirror cube, I suppose). I've also done some thinking on an octahedron corner-turning 3x3.

Depending on how you value your labour, the cheapest option will be to not cast anything and simply order everything from Shapeways.

To add onto the discussion. I do feel that casted puzzle material has a better feel compared to Shapeways material. I haven't personally handled any Shapeways puzzles yet, but from videos that I've watched, they just don't seem to be as nice of a material (possibly too textured/rough?).