Of course if anyone who knew what they were doing could use the assembly Reflector and extract the JS or CSS. But that would be a heck of a lot more work than just using something like FireBug to get at this information. A regular end user is unlikely to have the desire to go to all of this trouble just to mess with the resources. Anyone who's interested in this type of thing is likely to be a malicious user, not the end user. You have probably got a lot of other problems with regards to security if a user is able to use a tool like the assembly reflector on your DLL because by that point your server's already been compromised. Security was not the factor in my decision for embedding the resources.
The point was to keep users from doing something silly with these resources, like delete them thinking they aren't needed or otherwise tamper with them.
It's also a lot easier to package the application for deployment purposes because there are less files involved.
It's true that the DLL (class library) used by the pages is bigger, but this does not make the pages any bigger. ASP.NET generates the content that needs to be sent down to the client (the browser). There is no more content being sent to the client than what is needed for the page to work. I do not see how the class library helping to serve these pages will have any effect on the size of data being sent between the client and server.
However, Rjlopes has a point, it might be true that the browser is not able to cache embedded JavaScript/CSS resources. I'll have to check it out but I suspect that Rjlopes is correct: the JavaScript/CSS files will have to be downloaded each time a full-page postback is made to the server. If this proves to be true, this performance hit should be a factor in your decision.
I still haven't been able to test the performance differences between using embedded resources, resex, and single files because I've been busy with my on endeavors. Hopefully I'll get to it later today because I am very curious about this and the browser caching point Rjlopes has raised.