I think there is a tendancy for some - but by no means all - trained academics to come up with a theory and then search for evidence to support it.... rather than vice versa.
Personally I think a combination of reasons accounted for the distruction of many of our 'robbed out' cairns; treasure seeking, reuse of the stone in construction projects.... perhaps even some cult of symbollic desecration to uncover cists sometime in antiquity? Then, of course - here we go again - the actions of walkers upon the upland cairns.
I agree with Cerrig in that I've come across many a 'disturbed' cairn with pretty hefty dry-stone walls near-by. Probably not coincidence. Not to mention numerous long cairns with chunks taken out, the monument basically used as a quarry. Dowth is a prime example of this, plus the much reduced area of the great Heapstown cairn in Sligo.