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I am unaware of any studies or recommendations on how to tag boxes of pills in blister packs with foil. You are correct that if you were to place a tag on the bottom of a box and stack other boxes on top, you would not be able to read the tag because the aluminum layer would block the energy from the reader. To address this issue, you must consider several factors, including the tag used, the tag placement, your business practices and your data requirements.
It might be possible to place a tag on the edge of the box, so selecting a tag that would fit there is important. If the items were stacked with the tags facing out and no other boxes were in front of them, then you would be able to read all the tags. If boxes were stacked one in front of another, then the question would be whether you could could change your business process to read the tags before the next batch was stacked in front of the first, or whether there would be a way to read the tags as the pills were being put into the container. If workers were to pick up pill boxes and put them into boxes on a table, it might be possible to read each tag with an antenna under the table as the items were being placed into the box.
Consider your data requirements. Would you need to know that a box had been removed from a cabinet or carton? Or would it be enough to know that a carton of pill boxes had arrived and was now in inventory? If the later would be sufficient, you could tag the cartons of pill boxes. This should not be challenging, unless a carton was placed at the center of the pallet and you were trying to read it.
Some of these issues also exist with liquids. Water would absorb RF energy in the UHF spectrum, and the antenna of a tag placed close to a liquid would be detuned because water conducts electricity. The solution would be to place the tag in air gaps between the bottles. With the right combination of tag, tag placement and business process changes, you should be able to capture the data you need.
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