Don't forget that Low Tech electronics (TL5-6) are probably immune to EMP. Vacuum tubes don't get fried like modern electronics do.
Harry Turtledove wrote about this lack of effect in his "In the Balance" book of aliens invading Earth during WW2. The EMP knocked things off line, but no damage, they just started them back up and kept going. Planes and other things that are run by computers today were not effected because nothing was computerized.
In Traveller, I would say that most/all military hardware would be shielded from EMP. After all, at TL 6, an EMP is a pretty low tech weapon that in Traveller has been around for a LONG time.
Civilian items could easily be shielded for a few extra credits.