As a general rule, the activities on Extra adventure don't count towards achievement completion.

I wish they did as I just completed 2 gamethroughs, first time I used a hint 2x if I recall correctly, second time I didn't at all.
I've still not gotten all the achievements.
I'm getting a bit tired of redoing it because I wanted to skip the scenes in the first playthrough anyway as I'm an impatient person X'D But I don't know about doing it a 3rd time when it's not acknowledging when I've finished all puzzles.
I will have to do the game another 2 times to get all achievements assuming it picks up on my lack of hint usage next time and it's be more satisfying to just do the activities alone as it's really dragging and making the game feel less fun :(
If there was a lot of mystery to unravel that you could learn on multiple plays then I wouldn't mind but it's a pretty straight forward game.