I've found it depends on the "x" height.
There's something neat about having the tops of the (main) accents on the lc/sc line up with the top of the caps. Whatever it takes.

I think in general SC accents should match the UC ones, because:
- The congruence with the UC accents in an all-caps line is nice (since that's basically display usage, where congruence is central).
- In mixed-case setting SC are generally used for acronyms, which tend to be less accented; and anyway mixed-case text is more divergent (which is related to textiness) so it's less disruptive to have two kinds of accents.

Of course if you can have two sets depending on how they're used... ;-)

hhp