Is there unmanaged code in the Agility Pack? If so, will I see any problems using unmanaged code in my application?
No HAP is 100% managed code. It's even supported in Mono, which is the cross-platform equivalent of the .NET platform.
It's available as a C # source, so I don't think so. You will need to check extern s, but that's something like this ...
extern
I just took a quick peek into the code as it was convenient for me - I couldn't find any externs or any DllImport instances (since 1.4 beta 2).