As it is scribd is an embed/iframe, I think google considers my page as being empty with no content; google does see iframe content right?
From Google's help page about frames:
Google supports frames and iframes to the extent that it can. Frames can cause problems for search engines because they don't correspond to the conceptual model of the web. In this model, one page displays only one URL. Pages that use frames or iframes display several URLs (one for each frame) within a single page. Google tries to associate framed content with the page containing the frames, but we don't guarantee that we will.
If you are not the only site that is using this scribd iframe, Google may attribute that content to some other site, or even scribd itself.
Firstly, I am displaying the first pages of the pdf and the latter may be hosted on other websites, will this be considered as duplicate content.
Yes, this is certainly duplicate content. Your probably won't get penalized for the duplicate content, but having the text on the page isn't going to help you more than showing the iframe with it from scribd. When Googlebot find the content in multiple places, it usually indexes just one of them. Unless your site is the original, most authoritative, or most usable, Google will probably choose another site. For more information see What is duplicate content and how can I avoid being penalized for it on my site?
I am hiding the content and replacing it with the scribd embed with JavaScript; is it considered bad by Google?
Showing different content to Googlebot and users is considered "cloaking". Google penalizes cloaking much more readily than duplicate content. In this case, you are attempting to show Googlebot the same thing that you are showing users, so you might be fine, but there is still some risk.
