Bringing in birds always carries the risk of bringing in pests and disease.
Most birds(including existing birds) can carry disease(s) without showing symptoms until stressed.
Cleanliness helps but will not always prevent outbreaks.
Reasonable cleanliness-keeping things dry and well ventilated...
....you can't really 'disinfect' a chicken coop, unless there is specific organism that has been positively ID'd in quantities known to cause problems.
Unneeded medications, or medicating for something not positively ID'd can cause stress and resistant organisms.
IMO it's a balance, many things can't be eradicated, so you 'manage' them.