Personally I store only miscellaneous junk in shoe boxes.
Any painted figures I have or will get are or will be stored in figure cases.
I simply do not treat painted figures of any types as toys to be trashed by jumbling them up in shoe boxes, especially if I have painted or repainted the minis. My time is more valuable than that.
As for durability, no figure is going to handle careless abuse, such as tossed in a shoebox, very well, nor will the paintjob survive very long.
Simply put, if you value the figures treat them well. If you think of them as disposeable junk, treat them as junk.