Are you suggesting that the second half of the EoJ shot should be nullified by the shield?
The shield is already the ultimate denial tool; the EoJ is kind of the only effective weapon - it nullifies TB charge, a large amount of MC shot (which has to be accurately delivered).. it's a hard counter to most things. Not having the secondary hit of the EoJ would mean that only the first half did damage, right? which is 200 per shot. Five accurate shots with the EoJ, probably at range, to kill a guy with a shield..
I already find the shield frustrating to play against - my regular loadout is MC+TB, so if someone's running away with my flag at reasonable speed with a shield, I'm quite #@$!ed. My only hope is that they are intercepted by a teammate or they lose speed and I have a speed gate still up and somewhere useful. The likelihood is that I'd catch up to them by halfway up the map if I'm lucky - it's also likely (or should be likely) that they have cover fire on me as I chase them, so by the time I reach them they can probably just duel me, but if they don't, it's difficult to drill through their shield while they're fleeing... It literally feels like there is no outplay to the shield in that scenario, other than for me to change my loadout.
Even if I had the EoJ, a player at speed is a difficult shot, and if the capper has any sense they'd use their shield to get away from the base and then just snake their way around with a grapple. There's an argument here to say that our base should be better defended, and I'm fine with that observation, but as it stands people don't take roles quite like that - our PUGs don't have that level of coordination. All I'm saying is that in the games we have each week, going against a fleeing capper with a shield is a common occurrence and it's an irritating hard/flat counter to.. most things. Not even mentioning the cool secondary feature of the shield bubble, which is also pretty useful.
I find the TB to have a similar dynamic - there aren't too many places on the map where you can easily get away from someone that has stuck you, unless you have the shield. For the TB user, a shield is a crazy amount of denial - for the TB victim, if you get stuck you're pretty doomed unless you have shield or a decent amount of cover fire.
In regular duelling, the shield isn't as useful, unless you can drag out the time it takes an MC full-auto to batter through one, to the point where it's near overheating. If you can manage that, the shield then allows you to absorb that damage and then counter with a non-heated MC full-auto once theirs is near overheat.. TB duels get messy when a guy has a shield - becomes a game of hard counters.