In a purely military/reconnaisance sense one would assume that the Egyptians would have been primarily concerned with watching the obvious invasion routes. In desert terms, that would have meant somewhere that had sufficient watering spots within a reasonable march of each other. No army at the time could have carried enough water to cross the Sahara using the kinds of transport available.
However, it certainly makes sense that small scouting parties would have been sent out on expeditions to see exactly what sort of other watering holes would have been out there. Military commanders of "quiet" districts would have had little else to do except send out patrols to watch out for trouble.
Your last point seems logical. The Sahara is still drying out so it is only reasonable to assume that it was "wetter" 5,000 years ago.
Okay...maybe not that wet.
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