From a pure modelling perspective, CosmosWorks 2004 was not able to analyse multi body parts. I would imagine 2005 or 2006 can do this.
The question is, will it be oversimplified? Chances are Cosmos will look at the joints as simply bonded. If your welds are full penetration with no fillet, this may be acceptable. If not, you may have to add material to simulate the weld bead. If you are not overly concerned with the stresses in the welded region (more so concerned with deflection), the simplification may be acceptable.