Viscosity
No lubricating agents => No viscosity
The typical superlubricating bearings in gemstone metamaterial technology do not contain grease, oil or any liquids. At these lowermost possible size scales any kind of lubrication medium molecules would be as big as gravel. Crystolecule bearings run dry in a vacuum. They are either sliding sleeve bearings (fully wearless) or rolling gear bearings. So in this regard the viscosity of fluids is not of concern for nanofactories or gem gum tech in general.
Phonon viscosity
In dry running superlubricating bearings there is a relevant energy dissipation mechanism called phonon viscosity that is not related to molecular liquids. See main page: Friction
Viscosity in feed-stock supply
Only in the operating step of filtering resource molecules from a feed-stock solution liquids are involved. There diffusion is also involved in in replenishing resource molecule concentrations.
Note that this eventual speed limiting filtering step is not involved in the recycling of already mechanosynthesized and assembled microcomponents.