Although you can generate both 32-bit and 64-bit ClickOnce package, have in mind that your standard launch page will not be able to find out if an user runs it from a 32-bit or 64-bit computer.

Having said that, and knowing that the 64-bit ClickOnce won't run on a 32-bit computer, it makes sense to prepare always the 32-bit ClickOnce, that runs seamlessly on both 32-bit and 64-bit platforms.

You can however create two launch pages, one for 32-bit and another for 64-bit ClickOnce package.

Mark them clearly as such to avoid any confusion!