Nanites are microscopic robots that can do nearly anything they're programmed to do, within limits; it is not a near-miraculous technology that can be used to do absolutely anything. Nanites, specifically in the Federation, are used for advanced engineering and medical applications but as a supplement to bio-sciences, not instead of.
Nanotechnology in the Chakat Universe, and its applications, depends on the civilization. The Stellar Federation has a working knowledge of the subject, and they have several types of nanites, but these typically perform simple targeted tasks: medical nanites might be used to destroy a tumor, or alter a single organ... but the capacity to significantly affect an entire body using nanites has not been developed. Terran engineers of the 21st and 22nd centuries focused more effort into developing advanced biotechnology, especially in the fields of genetic engineering (creating morphs) — as a result, nanotechnology and cybernetics was sidelined, and developed gradually. 24th century nanites cannot perform miracles, and are simply tools occasionally use in medicine and manufacturing.
The Federation lags significantly behind the level of nanite sophistication seen in the Stariionae: their entire bodies are composed of extremely versatile and advanced nanites, in the same manner as organic creatures are composed of cells. This discovery has forced a necessary adjustment to the definition of "life form"... and with the help of Star Dancer and her two younger half-siblings who remain at the Star Home space station in the Chakastra system, Federation scientists continue to study the unique and fascinating Stariionae nanite-based anatomy and physiology.