Most FEMAP users would create two Rigid Spiders, Nastran RBE2s, and then connect them with a beam element where the beam is defined as a circular cross section matching the bolt's diameter. One can then apply a bolt preload to the beam element. In a mechanical assembly where there are mating faces, these can be put into Linear Contact. Nastran solves for the preload condition first, and then apply other loads after the initial preload condition has been solved. On the post side, since they are beam elements, and as long as one recovers forces from Nastran (which is the default), you will be able to query the beam element for total axial force and shear.
In the Custom Tools menu, under meshing, there are a couple of APIs written that can help do this. In sheet modeling with shell elements, there is an API Hole to Hole Fastener, that will ask you for the curves on one side of a hole, then the other, and will create the rigid elements and beam automatically. If you are working with solids, there are APIs in the Meshing section call Spider Surfaces that will create the rigid elements, you will have connect them by hand. I believe one of the FEMAP team members is working on an Hole to Hole for solids that will fully automate that as well. As soon as it is avaiable, I will make sure it gets e-mailed to you.
The process is more easy using 1-D CBAR/CBEAM elements as bolts bolts + rigid elements RBE2 to connect the bolt end with plates. Please note in this case you need to create surface-to-surface contacts as well: