First think you should do is login to that account when she is not around and forward all the emails to your own private email account. Clear out the evidence of this action from her email account if it tracks sent email.
You don't need to check the email account to know if she has been emailing him, because you already installed a keylogger. Just look through the keylogger history to see if you find the log of an email she wrote to him. If not, wait a while until you see what she is writing him.
Find out who the OM is, and if he is married, where he works, etc.
Should I send her an e-mail to this account telling her that she needs to be honest and delete it?
She won't give a damn. If she's into the A like it seems she is, your words will only annoy her. She'll find another way to hide her affair from you and you'll be left wondering again.
Should I call the OM to tell him to respect her decision?
What decision? You might have been under the
impression that her decision was to not contact him, but she lied to you. No one is forcing her to look at that email account, she is
choosing to allow contact to continue. He is not the problem, your wife is.
Gather your evidence. Are you monitoring the telephone? Consider going to Radio Shack and getting a voice activated recorder hooked up to the phone line, it's very easy to setup and it'll record all phone calls from home.
Plan A is for you, it's not something she participates in. Read up on it again and hold on.
Have you exposed at all to this point? Does family, friends, coworkers know about her affair? Once you have gathered some proof of continued contact you'll want to get a plan for exposure if you haven't already done so.
Good luck.