There’s less than 20mm difference in wheelbase between my 26″ Whippet and my 29er Race bike, yes the whole bike is some 3″ longer but that’s at the wheel ends, the tyre contact is in roughly the same place so for me the perception that 29ers are more of a handful through the tight stuff doesn’t hold up.
Wheels are more likely to flex more but for robustness I’ve never had any reason to question them. Smaller incident angles over the same rocks, bigger tyre volumes and higher axle centers seem to be more than enough to compensate. There is also more free length of spoke to take the strain as the wheel deflects in its rotational plane.