Hello,
1. This applies only to help pages. The thing is that help pages are stored as static HTML pages and served as static content. The pages that are not served as static content do not allow framing by default.
2. Session cookies cannot be marked with the Secure flag because cookies marked with the flag can be sent only over an encrypted channel (HTTPS). Currently, all security sensitive cookies are marked with the HttpOnly attribute. Starting from the next major version, Adaxes 2015.1, the authentication mechanism will be changed completely, and such cookies will not be used at all.
If you want, as an additional security precaution, you can enable SSL for Adaxes Web interfaces. This can be done the same as for any other IIS web application.
3. Currently all security sensitive cookies are marked with the HttpOnly attribute. The cookie that you are talking about is probably a cookie named AspxAutoDetectCookieSupport. This cookie is a part of .NET standard mechanism for detecting whether the client browser accepts cookies. We cannot mark this cookie as HttpOnly, however this is not necessary. The cookie does not contain any security sensitive information.