> will the linking command not already be generated at line 51 ?

we simply extend linking, no problem in cmake

> does include_directories not add the superhirn include directories to the global list of include dirs?

As it is a subproject it is scoped

> will then all following utils be using the superhirn include directories, defeating the purpose of modularisation?

see above 


> do the superhirn include directories now also include the GUI include dirs (from line 59)?

Sadly, yes. Fixing this would require an upgrade of cmake to 2.8.11