It is not normal to include welds in analyses. This is because most structures are designed to codes or standards which require nominal or hotspot stresses. The codes then take into account the strength/weekness of the welded connections.
Most models would only require joining at the intersection to transfer load. The stresses at the intersection WILL NOT be accurate so they should not be used. Be guided by the code on how to interpret the results or alternatively see the rererence listed below.
Niemi E; 'Stress Determination for Fatigue Analysis of Welded Components', Abington Publishing for the IIW, 1995, ISBN 1 85573 213 0.
Sometimes if the weld is large compared to the components being joined the stiffness of the weld itself needs to be accounted for. Often beams are used to add this stiffmess, the beams representiong the weld bead.
TERRY