It depends on the game really.
The last time I finished a jRPG was FF7 around ten years ago, and I didn't bother with all the super secret extra bosses.
I beat Twilight Princess with less than maximum hearts and other stuff, but that's probably because I played it through in like five days, and have been regularly coming back to get the last few collectibles.
I refuse to beat Okami without getting every single stray bead, which is pretty much the only reason I haven't managed to beat it yet, despite been able to go for the final boss for absolutely forever already.
In proper wRPGs like Baldur's Gate I usually get pretty much every there's to get, but remember skipping quite a bit of that stuff in Fallout and Avernum 3.
Conclusion: I dunno, mostly?