Oh, I'm with you on that. Only in one game did I talk to every NPC available after every event, and that was Trails In The Sky, because every NPC was fleshed out. It was still a pain. But I don't think the solution to the problem is to not have real NPCs or multiple layers of dialog, instead have notifcations showing you unread dialog.
There is nothing worse in JRPGs than talking to every NPC, except perhaps entering every house hoping for a golden chest so you can rob some poor family. No, clicking on all the NPCs is worse, because everytime you finish a story event you need to recheck all the stupid NPCs to make sure they didn't get new sidequests or want to give you something.
And the worst is when they have like 5 lines of dialog, so you try to click through it all, but accidentally click an extra time and start them over.
I guess I'm okay with ones where they have a ! over their head if new dialogue, like you suggest, but honestly I'd just prefer towns were a damn menu system.
A game like Dark Souls has all the plot I need -- that is, it's there if you look deep but it never gets in the way, relying on atmosphere/environment instead.
I can't tell you how many JRPGs I've finally gotten around to booting up and playing, but turn off after 5-10 minutes because I'm sick of clicking through dialog and haven't even been able to move, let alone fight, and the game is never to be played again. I just want to tell them all, I don't care what your problem is, I don't care who did what, just let me go kill everything and your world will be saved, so shut the hell up and let me get to it. If you have a sidequest just jot it down over there, and if you have something to give me, hand it over. Silently.