Do the Necromancy perks (under Conjuration) only affect reanimated corpses, or do they also affect summoned ghosts/shades? (Without getting into spoiler territory, at least one power and at least one specially-conferred spell allow you to summon ghosts…)

Well, the Atromancy perk affects the Conjure Dremora Lord spell, so I would assume yeah.

I'm completely ignorant on this (duh, I'm a random internet user), but I'd imagine that it effects only summoned corpses.

Considering the normal structure of TES magic effects, I'd say that anything you can turn undead on is effected.
I don't think I've ever used turn undead on a ghost, so I can't help you out here, but I'm sure somebody else has.
Anything that banish daedra works on is effected by Atromancy, for example.

Edit: Meaning they probably use flags for 'daedra' and 'undead'.

Good point. By that logic, if silver seems to do extra damage to my own ghosts, then that might be a good sign that they count as undead.

(Of course, I coud also just save, take the perks, test for duration, and then reload if they don't work. But for some reason whacking things with silver seemed like the logical follow-up.)

In case anybody stumbles upon this while searching: neither the atronach perks nor the necromancy perks affect a certain spell that summons a shade to fight for you.