Hi Viday,
1) What part of security do you mean ?
The security settings for uploading are always those, relating to the user ,who logged in (or mounted the networkshare). The Targetspaces have a set of security rules, which apply to all content inside, if not set to different settings explicitly. Upload can be done via HTTPS
2)
Alfresco does not care, if its a folder structure inside the zip file. You can define business rules, acting on content objects, beeing files or folders. In these rules, you can trigger workflows or start actions as well.
3) Do you mean a thumbnail or a reduced content preview ? (e.g. The first 3 slides of the PPT) ?
The first one is possible.
The second one isn't
Thirdly, you can use a flash-preview of the content. Go to the alfresco website and do a "testdrive" for Alfresco Share to checkout your formats.