Huiying,
1) as I don't know Nastran, I'm figuring out what your model would be in ANSYS. If I understood well, then the high stresses you are getting on the holes ARE calculation hot-spots.
2) if you want to examine the bolted joint with FE, build a "full-geometry" model where the bolt itself is also a meshed solid. Then, apply "contacts" btw bolthead lower surf and part surf, btw nut surf and part surf, and btw cyl surf of bolt and cyl surf of holes. In order to simulate pretension, a number of solution exist (in ANSYS you have a special option for this), but the most straightforward is to apply a negative thermal load to the bolt only, so that it shrinks down (but you have to define anisotropig thermal expansion coefficients, because you want the bolt to shrink only in the axial direction...)
3) if you have a complex interconnected structure, and you want to calculate analytically a joint but you don't know the forces on the connected members, then these forces will be the elem nodal forces (summed or integrated in some way depending on how your model is made, of course) that the two members share at their "interface" in the FE model
4) in the "weak members' material" you describe, VDI norms would have you redesign the joint (more bolts, lower pretension, bigger diameters,...) so that the ultimate strength (lowered by the safety factor, of course) is NOT reached for ANY of the components. If you are making a design "pushed to the limit", then you may want to account for the stress redistribution, local plastic deformation, and so on. In order to do that, the same kind of FE model described above is needed, with the difference that the solver wil be set to non-linear and all the material properties will include the non-linear part (which way depends on the constitutive laws that you can define within your FEA).