  (Abridged) We here investigate, by means of fully 3-D Smoothed Particle
Magnetohydrodynamic numerical simulations, the effects of magnetic fields on
overdense, radiatively cooling, pulsed jets, using different initial magnetic
field topologies and strengths ($B \simeq 260 \mu$G-0). The relative
differences that have been previously detected in 2-D simulations involving
distinct magnetic field configurations are diminished in the 3-D flows. While
the presence of toroidal magnetic components can modify the morphology close to
the jet head inhibiting its fragmentation in the early jet evolution, as
previously reported in the literature, the impact of the pulsed-induced
internal knots causes the appearance of a complex morphology at the jet head
(as required by the observations of H-H jets) even in the MHD jet models with
toroidal components. The detailed structure and emission properties of the
internal working surfaces can be also significantly altered by the presence of
magnetic fields. The increase of the magnetic field strength improves the jet
collimation, and amplifies the density (by factors up to 1.4, and 4) and the
H\alpha$ intensity (by factors up to 4, and 5) behind the knots of jets with
helical field and $\beta \simeq 1-0.1$ (respectively), relative to a non
magnetic jet. As a consequence, the corresponding $I_{[SII]}}/I_{H}\alpha}$
ratio (which is frequently used to determine the excitation level of HH
objects) can be decreased in the MHD models with toroidal components relative
to non-magnetic calculations. We also find that the helical mode of the K-H
instability can be triggered in MHD models with helical magnetic fields,
causing some jet wiggling. No evidence for the formation of the nose cones is
found in the 3-D flows, nor even in the $\beta \simeq 0.1$ case.
