The nut in question is torqued to a specific amount after all valve geometry and clearance issues have been resolved. The intake manifold is already in place and bolted down to specs before the rocker shaft final assembly. The rocker shaft end stand adjustment's, to get the right height, is a crucial step. Once that is determined all rocker shaft support stands are then torqued following a pattern at a specific torque setting. Final valve adjustment can now be set and the rocker arm cover installed (button it up). If it's a "long block" (assembled block, heads and intake package, in the case of an FE) it is now ready to ship. Or, it is now ready for final assembly work, carb, injectors, dyno, etc.
As the rotating assembly would have been balanced previously vibration should not be an issue. Heat cycles should not have an impact on the shaft retainers and mounting assembly fasteners. Excessive spring pressures, due to a "wild cam" should not be a factor (providing proper torque specs were followed). All these things are taken into consideration by the rocker shaft assembly design. Of course some designs are better, stronger than others, but not generally the SHAFT itself, that is fairly "generic" to most FE's (and relatively inexpensive). If a shaft mounting fastener comes loose, for what ever reason, the shaft WILL break in a hurry. It is under a great amount of pressure, and has been carefully designed to handle it.
Re-torquing of these shaft components, while perhaps a good idea, is not called for. Checking for valve adjustment would be logical at about the 2,000 mile mark, some check it earlier, some later. In any case, there should be no valve adjustment actually needed beyond a few thousands of an inch. If the valves are out of adjustment very much beyond that, you have a serious problem. Like a broken rocker shaft or a receeding valve seat, loose fasteners, a bent push rod, a broken or worn rocker or numerous other causes.
I've never personally used something like "LocTite" on the rocker arm shaft nuts/bolts, perhaps it's OK if you do? Maybe I've just been lucky? I wouldn't say it's standard procedure as there is generally no problem with these nuts/bolts loosening up over time (especially at 2,000 miles). Rocker arm shaft re-torque is not a standard procedure, a good idea perhaps, but generally not required or noted as necessary in warranty paper work.
I am NOT a professional engine builder, just an above average "back yard" wrench I guess. I have not worked on a ton of FE's, so I'm not an expert. But I do know what is entailed here, what needs to be done, what should have been done. Based on that, in my opinion, it's defective workmanship on assembly.
Barry R., Kieth, Brent and many others could perhaps offer a better explanation or speculate more accurately on the cause(s) of this "loose nut". Most troubling here is the fact that other loose nuts were found as well. Maybe the motor was built on Friday, final assembly minutes before punch out time?
You may not actually SEE a broken rocker shaft on an FE, by the way. The engine, following a valve adjustment, may run well! You could go for many many miles before you figure out you have a problem. Often there will be no additonal damage to any other components. No metal debris through the engine, nothing that "stands out" and makes you look twice. It is interesting that in THIS case it was a sudden and pronounced failure that led the owner to conclude, "Wow, something just blew."