When I computed the N*N coherence at the source level, should the source be rectified before the coherence computation?
No. Applying an absolute value alters the frequency contents of the file and makes coherence analysis impossible.
Note that connectivity analysis at the source level might be very complicated, and does not necessarily give more information than connectivity analysis and the sensor level. All the information is already present in the recordings, regularized minimum norm solutions destroy some information and introduces a massive amount of linear mixing between the signals, making the connectivity analysis more difficult (more signal, more linear mixing).