Is NM (Romex) wiring ok for a shop wired in 2006?
Determining whether NM cabling is permissible can be surprisingly difficult.  

In my opinion, if this is an outbuilding to a residence, it's cut and dried:  


  334.10 Uses Permitted. Type NM, Type NMC, and Type
  NMS cables shall be permitted to be used in the following:
  
  (1) One- and two-family dwellings and their attached or
  detached garages, and their storage buildings.


As long as you don't go afoul of 334.12 Uses Not Permitted (service conductors, embed in concrete, wet locations, etc.) NM is OK for single family dwellings, garages, outbuildings.   

However, in reality there can be complications.  Again in my opinion there should not be in this simple case, but often there are complications, disputes, disagreements, etc.  For other than single family dwellings / outbuildings, the actual rules are convoluted involving building code construction type classifications, occupancy classifications, and the NEC.  Electricians, engineers, architects, and inspectors trip up on and argue over this stuff all the time.  

In your situation, my concerns would be 


safety 
issues with buyer's inspection when you sell in the future 


With respect to safety, properly installed, NM in a metal building is code compliant and generally safe, there's no reason for concern just because there's NM.  If it isn't installed in a manner such that it's protected from the sharp edges of the metal, that can be a concern.  The stuff that's stapled to the floor that's being used for storage sounds like a legitimate concern, but should be fairly easy to correct.  

With respect to a future sale, since the NM is code compliant, you shouldn't have to worry about much.  You only have to worry about a future home inspector, working for a prospective buyer, that doesn't understand the rules.  The buyer's home inspector may think NM is not permitted in metal buildings and put that on his inspection report for the buyer.  

If that happens, you can only try to refute the buyer's inspection report.  You could show them the applicable code section.  You could have your own inspector or engineer write up a formal report explaining why NM is OK.  You also may be able to refer to the permit and inspection records for the property with the local code enforcement.