If the zoning allows for the number of units,   I'm guessing they will have an answer such as 'The unit will need to be permitted and brought up to code as necessary'  which for an established unit will probably mean they look at things like presence of smoke/CO detection devices,  window egress requirements,  and other basic safety and habitabilty requirements. 

it is not necessary to delead a a building to comply with the federal LBP rules though some local jurisdictions require certain uses such as day care to be "lead-free" meaning that no lead paint is present-even the underlying layers of paint. the customary technique used in phase 1 assessments are lead swabs but they do not detect buried layers of lead paint.

For me, that was a marketing and sales business that was highly systematic, and fine tuned to have no real bottlenecks early in the businesses' lifespan (besides data, which takes some detective work).

As an ex-smoker and knowing many people who quit, I assure you over months or years, the smell dissipates and you cannot detect any odor.

The moisture detector once we put fans in the ceiling for a few days now detects no moisture.

I would recommend Home Detective Properties.

What are problems that can be detected and what are problems that can never 100% be caught regardless of my due diligence?

I have my brother in law call the realtor listing the property to do some detective work.

Call the local detectives/police to get details on crime, etc. 

Once you know who your seller is, with a little bit of due diligence and detective work, you can almost always find out the REAL reason behind the offer to the market.