I don't know about pdf files, but text inside an IFrame is not indexed by Google. I believe Google does follow links inside IFrames.
Oddly, I believe, the <embed> element is deprecated in HTML4 but not in HTML5? The <object> element was preferred.
I could only guess that by virtue of its name Google would index "embedded" content.
There may be security issues/ differences on how browsers handle material in these two elements for content on and off site. Iframes may be alright for off-site content, but "embed" may have security issues for off-site content. Not at all sure about this.