first case: I probably would just passivly 'accept' the mileage credit (if it would be on my LH miles&more account, I would tell my local LH angels, and they would probably say: 'thank you for telling us' and 'enjoy' - they did so in the past)

1) I buy a Y ticket, but get bumped to C at check-in. What happens if I send off the C stub? (Flight miles already registered as Y.)

my experience with all StarAlliance carriers (and LX and KL): they will only credit the miles for Y, and not change that after you send them the C stub (as the C stub is, int heir records which they will check, still shown as an upgraded Y stub). Wrongly higher credits can (as an exception) happen, if the agent 'doing' the upgrade/rebooking does that wrongly.

2) I get a cheap round-trip and fly one way only. Is there any way of getting points for the return leg, short of checking in and then no-showing? (And were I to do this, how I can I tip off the airline to not hold the plane for me while not sabotaging my mileage?)

I never got (accidently) credit for 'throw-away' practice. In add you risk other 'sanctions' doing so. A very good friend of mine, when 'having' to throw away the last segment, plays the game as follows (and doing so was never 'punished' with a later higher fare etc):
a) at his final stop (before the 'throw away-segment') he goes to a ticket counter and says that he unfortunately can't take the booked last segment (or return segment) and that he expects to get a refund
b) getting (the expected) answer, that no refund is possible, he, with tears in his eyes, very much regrets and says, that he is disappointed, but still, for the 'sake' of airline-management, the agent should nevertheless cancel his last sement ...