I have figured it out:
Adding a %(RelativeDir) Item Metadata was the solution.
Maybe other will use it as an example. Corrected fragment is:
<Target Name="CopyUnprotectedFiles">
<!-- Copy unobfuscated file to "unobfuscated file".unobfuscated -->
<Copy
SourceFiles="@(ReactorFile)"
DestinationFiles="@(ReactorFile -> '%(RelativeDir)%(Filename)%(Extension)$(ReactorUnObfuscatedFileExt)')"
SkipUnchangedFiles="false"
/>
</Target>