Remilia must of thought Sakuya was dead. Or maybe she was joking.
Well we never saw Rumia after EoSD....[']
Even if you consider the Reimu-path as the "canon-route" of the game, it must have been a joke by Reimu/Remilia. Reimu and Sakuya may meet again in Episode 6 of Reimu's scenario in Phantasmagoria of Flower View. It kind of hints to the theory that Danmaku is non-lethal or that no one really ever dies in Touhou.
It is probably just another reference to Agatha Chrisitie's book "And Then There Were None". There seems to be a lot of those in EoSD. If it is then Remilia is most likely just asking "Are you the one causing the trouble in my mansion?" Just like how the murderer was causing trouble for those on the island.
Given that the whole point of the Spell Card system is that it enables non-lethal problem resolution, a.) No one dies in Touhou. b.) Remilia is therefore making a joke or an Agatha Christie reference.