I got the same email last night. The path clrearly existed. I opened a ticket, to which support has not yet replied.
The reply from support just arrived:
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I apologize for the confusion today. A batch of automatic WordPress upgrades to 3.5.1 failed due to an issue with one of our central controller servers. The error message generated due to that failure was:
The problem was directory /home/username/domain.com doesn't exist! Unable to upgrade!
As you've noticed that directory does exist and is just fine. The upgrade didn't change any files in the directory so each installation should be running an older version of WordPress still. Our admin team are going to re-run the upgrade process again for each of these domains tomorrow.
This upgrade feature is enabled for all Dreamhost One-Click Installations by default, however it can be turned off for each installation. To do that simply go to the Goodies > One-Click Installs section of the Dreamhost panel.
There you'll click Manage Installed Applications. Then click your domain and under Upgrade Action select No Action. Again I apologize for any confusion these messages may have caused. If you need anything else then please contact Dreamhost support.
The Happy Dreamhost Clarification Team