"Manage My Account" is broken from the Metaverse pages but that has nothing to do with your MV characters or empire, it only has to do with your Stardock user account. There's no need or special benefit of managing your Stardock user account from the Metaverse pages when you can simply go to the forum pages to do so.
However I do agree that it would be nice for this to work from the Metaverse pages as well.
But as far as MV characters and empires I'm pretty sure you can still do everything that you used to be able to do. I don't think you can actually delete a MV character once created but "Edit My Characters" allows you to change any character's name and logo, clear the scores of any character and make any character your default. I don't think that you ever could totally "delete" a character. Also once you've selected one character as default then you can certainly change that to another character but I don't think you were ever able to go back to not having a default character set, but I could be wrong.
As far as empire's you can still manage your empire from "Edit My Empire" but like characters you can rename it, change the status, change the logo, motto or website, but I don't think you ever could actually delete an empire, I think the closest you can come is to set it to "closed".
