What happens if Cassiopeia takes the magical footwear rune?

The rune's aren't disabled. Players are likely supposed to realize that the rune is worthless. If they don't realize their mistake, then it's their loss. This isn't really intentional though, more of a consequence. The game just doesn't (and in my opinion, shouldn't) detect if the player is selecting these runes when in champion select.

No. Making inferences from RiotRepertoir's remark above, the system will essentially perform a double negative. The champion has -1 boots, rune attempts to give boots, champion now has 0 boots.

As for manaless champions and spells, its attempting to refund 0. Like getting an empty cup from McDonald's and trying to take it back to get a refund.

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Does the system automatically switch them to something else?

yes. try it in a training game. it will just swap to a different rune.