NERD ALERT! Most virus' do not survive long on raw wood, as the wood breaks down the lipid structure of the virus matrix. 2 - 3 hours at best. The sanding process will kill off more of the 'bugs' as will the chemicals used in the various finishing processes. So, essentally the guitars can roll off the line reasonably free of viral nasties.
The biggest threat to exposure and transmission is between the employees themselves. As long as everyone wears proper respirators, and avoids sneezing and coughing on each other, everything should be good.