The problem with those the numbers is that they get stolen in rural areas. Case and point; almost no AZ 69 shields are stolen because it is the main connector road from I-17. US 666 on the other hand was in an area that has no population and had signs stolen all the time. Even something like I-69 doesn't get a ton of theft given the nature of how much traffic it has. Using 69 on the modern CA 245 corridor was a huge mistake, north of Woodlake to 180 you would be hard pressed to encounter another vehicle traveling the same direction.
Back in the day it was likely the Division of Highways either had little idea about the significance of the number "69", or, if the issue was brought up either at the district or statewide level, presumed that since there weren't any universities
that close to the route (save Fresno State), the "pool" of potential sign thieves doing it strictly for amusement was lessened; obviously, they didn't consider locals who were attending college elsewhere -- or that, in the turbulent late '60's, college students had a lot more on their minds than stealing sexually referenced signage (most of us
did fit that description). Since the CA 69 signage lasted about five years before the route was redesignated, it's likely the cost of replacement signs was the deciding factor regarding the change -- the process of which requires legislative rather than simple administrative action.
I've always wondered -- since US 69 and later I-69 traverses considerable rural mileage, if there's a problem with missing signage on those routes (as well as any state with a route 69); it would be interesting to do at least an anecdotal study (I don't know whether I'd go the the effort to do full regression analysis on such a seemingly trivial matter!) about this. Also -- I've wondered if the folks along the path of the planned I-69 (particularly those in the so-called "Bible Belt", through which much of the corridor travels), have lodged any concerns or objections to that particular number. Since US 69 was established prior to widespread discussion of such things (at least in public discourse), the commission of that route was likely without controversy.