Hi,
You can still use those templates, but you have to edit them with the html editor instead of the frag & drop editor.
In Configuration->Mail settings you have an option Multiple parts. When enabled AcyMailing will send the text and the html version in the e-mail so that depending on the recipient server, the appropriate version will be opened.
In v5 you could disable html on a per newsletter basis. That's something that has not been added to v6 yet, but it will come back for sure. So if you really need this, please stay on v5 until this feature has been brought back to v6.