I know, we may be used to think different with Helpdesk Software than OpenERP does :) But it works, I try to explain, how i got happy with this. Its still no replacement for other Helpdesk Software. But you can work with it:
If you have proper installed and configured the helpdesk module and the automatic creation of an new issue due an incoming e-mail: Open your new automaticly created issue called "YourIssue" (Project -> Issues -> "YourIssue"). You have to use the Menu "Projects". Not via Partner/Contact.
In the open Issue, on the Bottom, above the History, you can click to "Send a message". This is how you answer this E-Mail / Issue. Yup, you'll be missing the E-Mail Template and the "We received your message, your Ticket ID is: xyz". Take a look at this: https://accounts.openerp.com/forum/Help-1/question/31783/
If you just have to add an internal note, use "Log a note". Jup, i also expected some big "reply-buttons", but this is how the communication system in OE works.
Below the "Send a message" Button, there is a complete History of this Issue...I know, its not filtered to E-Mails only :( But if you click to "follow" -> "Discussion", you will receive further mails. Yes, it is still not a filtered history of the past...
This may be an interessting explantaion: https://accounts.openerp.com/forum/Help-1/question/35894/. There may be an approach
No, as far as i see, this Issue and all its History is "not yet" linked to the customer/partner.
If this helped a little bit and answered your question, please vote. It is just a little summary of ideas and answer to your question. it's not helpdesk replacement guide ;)