Directory structure

.
├── SConstruct
└── src
    ├── libA
    │   ├── a.cc
    │   ├── a.hh
    │   └── SConscript
    ├── libB
    │   ├── b.cc
    │   ├── b.hh
    │   └── SConscript
    └── SConscript

---------------------------------------------

# In SConstruct
SConscript('src/SConscript', variant_dir='build', duplicate=False)

# In src/SConscript
env = Environment()
SConscript(['libA/SConscript', 'libB/SConscript'],
           exports='env')

# In src/libA/SConscript
Import('env')

env.Append(CPPPATH=['.'])
env.SharedLibrary('a.cc')

# In src/libB/SConscript
Import('env')

env.Append(CPPPATH=['.'])
env.SharedLibrary('b.cc')

---------------------------------------------

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/libA/a.os -c -fPIC -Ibuild/libA -Isrc/libA -Ibuild/libA -Isrc/libA src/libA/a.cc
g++ -o build/libA/liba.so -shared build/libA/a.os
g++ -o build/libB/b.os -c -fPIC -Ibuild/libB -Isrc/libB -Ibuild/libB -Isrc/libB src/libB/b.cc
src/libB/b.cc:3:16: fatal error: a.hh: No such file or directory
 #include "a.hh"
                ^
compilation terminated.
scons: *** [build/libB/b.os] Error 1
scons: building terminated because of errors.