Interesting. At this point I suspect we can only speculate.
I think Carmike is right: as I remember (which, for my Halfzeimer's- afflicted brain, isn't easy), those Revell warship kits from the fifties and sixties came in a wide variety of box sizes. I think the sailing ships (what I grew up thinking of as the $3.00 series - the Constitution, Santa Maria, Bounty, Victory, Flying Cloud, Eagle, etc. - did originally come in boxes that were the same size. I can't remember much about the company's airplane kits, but I don't think their boxes were universally standardized either. I may well be mistaken about that, though.
I can speak to one particular example. When I was in grad school (about 35 years ago) I was rummaging through old copies of the periodical The Mariner's Mirror in the university library and came upon (in one of the 1936 or 1937 issues, I believe) an article about H.M.S. Bounty. It contained foldout copies of the Admiralty draughts of the ship - in scales that fit the paper on which the magazine was printed. I xeroxed one of the drawings, took it home, and compared it to the Revell kit. They were a perfect match; the scale worked out to 1/110.
Coincidence? Well, maybe so. I do know that at that time Revell had an incredible pantograph machine that did a brilliant job of reducing and enlarging parts - presumably from the hand-made masters. (There are several instances of parts - figures, for instance - showing up in different scales in Revell kits - but otherwise identical. And the masters for those figures in the old Bounty kit simply could not have been carved on 1/110 scale.) My guess is that the masters for virtually all the old Revell kits were made on a larger scale and "pantographed down." But that's just intuition; I have no documentation to reinforce it. And if all the masters were pantographed down to make the kits, how did the Bounty end up (a) on a weird, non-standardized scale, and (b) exactly the same size as that print in the Mariner's Mirror?
What does seem clear is that the people at Revell in those early years assumed that their purchasers didn't care much about standardized scales. Given the company's success, I guess that must have been true.
Another possibility: somewhere along the line some plain old sloppiness slipped into the process. I think the first generation of Revell warships were based on a series of "modeler's drawings" that the Navy sold, as a PR exercise, in the first few years after WWII. I've seen some of those drawings; they're pretty crude and basic - largely, presumably, because the actual plans of the ships were still classified at the time. If the kit designer working from one of those drawings intended to make a cruiser kit to 1/500 scale, it wouldn't take much of a mistake (in those days before photocopiers, and before one could change the scale of a drawing by punching buttons on a machine) to shrink it a little by accident.
All that is, of course, speculation and idle rumination on my part. I wonder if enough of the "old hands" at Revell are still around that we could find out. I suspect the first-hand knowledge of just how the company's design process worked is all gone now.