After moving my malt whisky upstairs yesterday and back down today (the least pleasant part of hosting the GBS World Whisky Day event!) I decided to put the bottles back on the shelf without the box or tube (if they had one).
To this point they have generally been kept in the box/tube but that tends to take up more space. Presumably being in the box provides a bit of extra protection from light. But these bottles are stored where direct sunlight never reaches them and are in a basement where the overhead light (a mix of fluorescent and incandescent bulbs) is on only a relatively limited amount of time. The ones that never has a box/tube don't seem any the worse for wear so far.
Any strong reason to put them back in their box or tube? Some will likely be there for awhile. Just too many to drink them all in the near future!
For the moment I am keeping the box or tube. Not sure how long that will last but if they ever have to be moved I thought it might provide some protection to put them back in their box/tube.