On the Closing Disclosure you have to include the date issued, closing date and disbursement date.

If you are providing the disclosures electronically (in compliance with e-sign) don't we still have to follow the 3 + 3 day rule in calculating the dates?

For example:
Date issued 12/15/16; Closing Date 12/22/16 (3 days to receipt, 3 days waiting); Disbursement Date 12/27/16 (this would have included Christmas observed).

OR can you assume that they will open it within 3 business days and disclose the dates like you would for in person?

For example:
Date issued 12/15/16; Disbursement Date 12/19/16; Disbursement Date 12/23/2016

I know that you can start the waiting period if you receive confirmation... I am just not sure how to disclose the dates, do you or do you not base it on the assumption they will open?

You could do it based on the assumption that they do not open it and then if they opened it early and want to close sooner, you would issue a revised CD at closing with the updated dates. However, if you already have a set closing date and are in contact with the customer and they know they have to open and review the CD by a specific deadline, you could go the other way. I see no harm going in either direction based on the best information known at the time of issue.