Anything that relies on javascript, flash, silverlight and whatnot is generally called a 'script' (for brevity, it's not necessarily the best description). When a browser sees a script it starts it, just like you start an exe when you see one.
What happens then is up to the script, in case of youtube for example a player gets started, a video downloaded and played. In case of an adsense block the script connects to a G. server and downloads links to be shown to the visitor.
A spider downloads the page and usually never executes these scripts. No videos, no contacting of third party servers, no popups, nothing. That is why you don't see impressions when crawlers visit your page. If you disable scripting in your browser you'll get similar results.
Bots also don't run any PHP scripts (like includes) but they don't have to. Your host assembles the page and sends the result. There are still traces of this procedure though as indicated by the presence of the bot="Include" tag.
So to summarize, bots can by all means see when you are using includes and it's a matter of preferences whether to penalize their usage. So far this has never been the case and search engines don't not consider includes duplicate content (but they also don't put them in their index).