Re: bolt-through locking nuts?
The top mount is susceptible to screw hole damage (wallowing out or stripping of the hole) from trem use especially if the wood screws loosen up from weather changes or whatever, and goes unnoticed. At that point though, you'll have tuning stability problems and it's usually easy to identify the loose nut as the culprit. Overtightening the wood screws can also lead to stripping of the holes. The good thing is, if the screw holes strip out, you can usually drill the hole through, add a counterbore on the back side and mount up the same nut (the holes are threaded) with thru-bolts.
Wood screws are great for pickguards and truss rod covers but for a component that sees a lot of stress reversals (e.g. locking nut under trem use), the clamped design (thru-bolt mount) is probably more reliable.
As for neck strength, the top mount could be stronger, but if the wood screws went in a little too tight on initial installation, cracks can develop.
At the end of the day, neither neck design will take the wrong hit on the headstock... best to avoid accidents with the guitar when leaning it on things, turning around in tight places, stepping on it in the dark, taking it off in a room with low ceilings or overhead fans, etc.