Yes, they are in IL - they launched Reflector , and you will see them. If they did not get into the IL, you could not build against them like libraries. (And yes, you can reference .exe files as if they were class libraries.)
However, all of this is permitted in JIT.
Keep the names readable so you can keep the code in the future. The performance problem is unlikely to make any measurable difference, and if you want to confuse your code, do not do this at the source code level (where you read the code) - do it using a specially created obfuscator.
EDIT: As for the included one - why not just run Reflector or ildasm and find out? From memory, you lose the local variable names (which are in the pdb file if you create it), but more on that. Private method names and private variable names still exist.
Jon skeet
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