I cant comment on the software as I have never used it.
EMI filters, ferrites etc are always a good choice when things are going or coming off board, most designs I do have an some sort of EMC, ESD protection for connectors.
As to EMC software, my view is learn all you can from people like Henry Ott, Keith Armstrong etc and lay out the board correctly so minimising any EMC problems. I very rarely have EMC problems with my layouts and do a lot of high reliability stuff and SMPS layouts, but I have spent 25+ years studying and learning...
The basic EMC thing to learn is to understand dipole structures on a PCB layout.