JM has it right and BTW, in my case I'm the one who hasn't closed the joint account yet, for the same reasons - direct deposit, re-fi going on and so forth would just make it easier to wait until the new ducks are in a row first.
I say if you want to be nice then TELL her first that YOU are going to do it (nicely). Then do it. Does she have a new account? If she doesn't, then that may be a problem. If she does have another, then say (in an e-mail if necessary but what the heck is wrong with calling her? Is there something worse she can do to you if you irk her?) "Hey, I'm going to close the old account Tues. Let me know if that's a problem"
BTW, don't know where in the D process you are exactly, but as I understand what you have said, you have both signed on the final agreement? Do you have to go to court? Is that waived? What I am getting at is there is stage past which she has less power to screw with you custody wise without starting a new battle in court. Also, I don't know your W, but is she likely to do that? Is she (or is she being) that kind of person? Maybe you are worrying too much.
I say call her and tell her you are going to "stop by the bank and take care of the account" and let her react. Time to stop walking on eggshells.