First use a joint, then use a beam.
To design a bolted joint, first you need to extract the forces and moments that go through that bolt during the applied loads.
A simple way to obtain the forces and moments is to use a Fixed Joint and request the Joint Reaction Force output in the solution. Yes, you could use a beam to get the same information, I prefer a Fixed Joint.
Using the forces and moments from the Fixed Joint, select a candidate bolt size using simple hand calculations. Select an appropriate torque for that bolt size. Calculate the preload using a Bolted Joint calculator.
Next phase is to replace the Fixed Joint with a representation of the bolt that can have the preload applied. This could be Beam elements or a 3D solid mesh on the bolt. Add the Bolt Pretension load to the model and make the model a 2-step solution where step 1 is Bolt pretension Load and Step 2 is Lock.
Now evaluate the results to see if the applied forces and moments can create a gap in the joint and if the shear forces can cause the joint to slip. You need to know the coefficient of friction between the faces that are being bolted together for this. A gap or a slip is considered a failure of the joint and the bolt pretension force is inadequate. Increasing the bolt pretension may require a larger size bolt. In that case, it is less work to edit the beam cross-section than increasing the diameter of a solid mesh of the bolt shaft.
The way a properly designed bolted joint works is that the bolt stretches a lot, while the flange material compresses a little. Any loads on the structure go through the thick flange material in contact and make tiny changes in the little bit of flange compression. Those tiny changes are insignificant to the bolt. The flanges never slip from the applied shear loads. That is why the bolt does not suffer fatigue failure.
In a poorly designed bolted joint either the flange slips, causing bending cycles to accumulate on the bolt, or a gap opens and closes between the flanges, causing large changes in the bolt stress. In either case, the bolt can suffer a fatigue failure.