Why are centrioles aligned at 90 degree with each other?
As far as I know, the function is not truly known, although there are some seriously interesting guesses.  Part of the problem seems, from scanning the literature, to be that it's not easy or obvious to disrupt centriole orientation.  This paper in PLoS Biology presents some really interesting results, in particular two piece of evidence:


Centriole orientation, to some degree, is dictated by the "mother" centriole during centriole division and is thus passed on from cell to (daughter) cell.
Defects in centriole orientation can result in organelle localization defects in the cell (e.g. nuclear orientation), and at least some of these defects are genetic.


So it seems that orientation is, in some part, a product simply of centriole division, but that there are some gene products that do help determine orientation and localization.  This paper puts forth the hypothesis that centriole orientation determines the axis of cell division which can affect embryo orientation, whereas this suggests that external environmental factors could translate into altered centriole, and therefore cellular, orientation.