This might be a silly question, but why are you trying to hide the humbucker? Aesthetic reasons?
The most popular reason is to save / retain the artwork on the top of the box .
I'm guessing that is the case here .
To avoid a microphonic . piezo type sound , mount the pickup so it is barely touching the lid . Remember to take into account string / bridge downward pressure not making it touch by spooning a bit etc if the lid is thin. . ..You can accomplish this by mounting to the neck inside but leaving a space between the lid and pickup . or you "could " "hang" it from the lid with rubber or cloth separations (as long as the mag part is not touching the wood .( mounting ears padded should be fine .).
your pickup will still read the strings even through 1/4 inch wood or more . make sure strings are not too high from the lid (around normal guitar action height ). a larger distance will weaken the signal more than thick wood will.
assuming this is a wood body ? and not a tin ?. cause that's a whole new animal ;-)
Could drill small holes or cut small slits in the top just over the pickup's poles. That would help with volume.