Horses can manufacture the many complex proteins and molecules they need from whatever food happens to be around. Again, they pay for this flexibility by having an intricate digestive system able to break down food into its constituent molecules, and a complex intermediary metabolism able to synthesize whatever they need from whatever they've got. The mechanical designs proposed for nanotechnology are more reminiscent of a factory than of a living system. Molecular scale robotic arms able to move and position molecular parts would assemble rather rigid molecular products using methods more familiar to a machine shop than the complex brew of chemicals found in a cell. Although we are inspired by living systems, the actual designs are likely to owe more to design constraints and our human objectives than to living systems.
Self replication is but one of many abilities that living systems exhibit.
Copying that one ability in an artificial system will be challenge enough without attempting to emulate their many other remarkable abilities. The study of artificial self replicating systems was first pursued by von Neumann in the 1940's. More recent work by Drexler continued this trend and applied the concepts to molecular scale systems. One conclusion from this body of work is that the design complexity of artificial self replicating systems need not be excessive. The estimate of the complexity of the internet worm is simply an approximation to the number of bits in the C source code.