This paper might be useful to making a determination if you need to consider secondary bending effects, or if simply designing as web members being pinned is acceptable (which it can be in many instances).
Link
Depending on the relative stiffness of web vs chords I often check both for piece of mind and to get an envelope of the true behaviour, which is probably somewhere in between.
If you are familiar with the direct stiffness method (as it sounds like you are based on your responses), then its a matter of selecting a member stiffness matrix which includes all the effects that you want to consider. i.e. if you want to include secondary bending (shear deformations, temperature, etc, etc as others that could be included depending on how far into it you want to go).
Then your formulation for the member and global stiffness matrix assembly includes terms for the bending & axial effects, rather than say just the typical axial member stiffness matrix that might be used for a pinned member that can only output axial forces and deformations.
At some point the complexity of it and the time investment involved probably does mean it is likely to be easier to simply use a commercial program, but for smaller problems you can certainly use excel and program the DSM quite easily if you know what you are doing.