Do you mean "Are CST and HFSS suitable to use to search for superconductors"? The answer to this is almost certainly no. Codes which can correctly describe the interactions between electrons and atoms in lattices are required, and don't exist yet.
If you mean "Can CST or HFSS predict the results of using superconductors?" I don't know, but I expect not, but COMSOL will be able to, but you may have to find the right equations and put them into COMSOL.
Mohamed Lamine Tounsi HFSS and CST are fully electromagnetic simulators that solve Maxwell's equation with numerical methods. Regarding superconducting materials, an interaction between atomic particles is certainly required.
You can try Multiphysics based simulation (Ansys or ComSol).
Otherwise, if you have the required datasheet, you can extract the data vs Freq in HFSS and check your simulation how it performs. In that case you will not get the atomic response like described above but an overall idea of your EM wave interaction.