Yes, you should leave k as 1.

No, you should not ignore the flexibility of the thin wall fittings as calculated within FEA. You just shouldn't input it through the k factor, but through CNODEs or through the nozzle flex feature.

I don't know what your piping system in particular looks like, but if elbow stiffness contributes to failure in all components (pipe, equipment, and steel, etc), it makes sense, sure.

But I can envision scenarios where this isn't necessarily true.

So, if you're certain that what you're doing is more conservative than reality, then yes.

After all, buying a dozen eggs when you only need six still means you can make omelets.