A couple of options for you:
First, scons likes to use SConscript files for subdirectories. Put an SConscript in src/
and it can refer to local files (and will generate output in a build subdir as well). You can set up your environment once in the SConstruct. Then you "load" the SConscript from your master SConstruct.
SConscript('src/SConscript')
As your project grows, managing SConscript files in subdirectories is easier than putting everything in the master SConstruct.
Second, here's a similar question / answer that might help -- it uses Glob with a very simple example.
Third, since it's just python, you can make a list of files without the prefix and use a list comprehension to build the real list:
file_sources = [ 'a.c', 'b.c' ]
real_sources = [os.path.join('src', f) for f in file_sources]