That is one of the limitations of an EICR. You sample test the sockets for tightness (say 20%) but you do not usually lift floorboards to test JBs (and probably would not know where they were)
Recently I did a lighting rewire and I used JBs as I was only able to get a 1.0mm down the conduit to the switches and loop in loop out at the lights would not have worked due to the type of lights. All the jb's are together under a floorboard (more like a trap door now as it no tongue and groove left) in the airing cupboard. It took a few hours extra to get them there and not just fit them where it was convenient for me.
This trap door is noted on the installation certificate and the customer even labelled up the CU with the info.
The upstairs lights are done the same with all the jb's by the loft hatch on a panel above the insulation that the customer installed for me.