Comments are stripped out on any kind of build. If you do a build in Release mode then debug info is also stripped and the compiler will perform optimisations on the produced code as well.
As for the Dotfuscator I personally dont see a lot of benefit - is your code (or most peoples code even) that special and fantastic somebody will want to decompile it?
It is normal for the config file to be deployed as well - this allows for some control over the execution of the program depending on what values you are storing in there.
Rather than storing the serial number in the app you may want to store a hash of the number and when the user enters the serial to unlock it hash that and compare hashes. (Have a look under System.Security.Cryptography for classes to do the Hash - MD5 or one of the SHA classes should be suitable).
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