What is Ctrl+Y?
Ctrl+Y is a common keyboard shortcut for redoing actions, it's opposite to Ctrl+Z, which undoes actions. Sometimes, Ctrl+Y is mapped to other operations, in which case Ctrl+Shift+Z is usually the keyboard shortcut for redo.
Considering the above, it would be an incredibly bad idea to have the default action performed by Ctrl+Y in an application to be an operation that modifies the undo history, e.g. mapping Ctrl+Y to deleting the currently selected layer in an image editor, since that would mean the user can't press Ctrl+Y, realize it doesn't redo, and then try Ctrl+Shift+Z, because when they press Ctrl+Y that would change their undo history and then they can't redo anymore..
Some applications, such as IntelliJ IDEA, display a dialog box the first time you press Ctrl+Y asking you which operation should Ctrl+Y be mapped to. How nice of them. This avoids the issue completely.