As you you've said that's normal since the file are located in a folder inside /usr/include, not directly into the include directory, anyway this has nothing to do with Eclipse or any other IDE but it's just a matter of GCC and the enviromental variable "C_INCLUDE_PATH" if you're using plain C or "CPLUS_INCLUDE_PATH" if you're with g++, if you really don't want to use the #include cryptopp/aes.h
sintax just append the /usr/include/cryptopp folder to the appropriate enviromental variable, maybe with a line like this one in your .bashrc file
C_INCLUDE_PATH= $C_INCLUDE_PATH:/usr/include/cryptopp
anyway, I don't really see any problem in using #include cryptopp/aes.h