We appraise the realty. Period. A structure is a structure and whether the current occupancy involves a religious use, sexual use, hobby use or personal hygiene use is nobody else's business until we get into structures built without the necessary permits or health/safety problems.
If I walk into a home and there's donkey **** and KKK propoganda playing on every TV in the house and lines of coke laid out on the coffee table none of that goes into an appraisal report because the personal characteristics of the occupants is not part of the valuation. I don't comment on "maintenance" because that speaks to what people do - I comment on "condition" because that relates directly to the attributes of the realty.
We're all human and we all have our personal biases with respect to the personal characteristics of others, but the moment an appraiser reaches a point where they cannot in good conscience refrain from commenting on this type of issue, that's when it's time to withdraw from the assignment.
My advice to the OP is that if the local authorities have signed off on the structure in its current condition then don't worry about the horticultural occupancy of the unit. That includes it's plumbing and electrical connections and systems. A meth lab is different because of the hazardous materials conditions. If the appraiser makes any noises you can remind them that appraisals are about the realty interests of a property, not the personal characteristics of the occupants. And then direct them to this thread to read up on the reasoning.