Blood substitutes can be substantially less complex than blood:
At the start of TNG, the replicators' abilities were ambiguous.
Afterwards, their abilities - and limitations - were crystallized.
As said, transportation!=creation.
The self replicating mines have a lot of problems: with their energy supply (and available matter) in the first place. The ability to replicate a computer and sensors (which are FAR more simplistic, informationally speaking, than biological living tissue) is a distant second.