1. Mmm, to the best of my memory, wasn't Zabuza somewhat just playing around with Naruto & Sasuke? I could be wrong, but if he was then that whole thing with Sasuke is bad information :3 For the second part, Konan is a long-ranged fighter, meanwhile Kakashi is a short ranged fighter. Konan wouldn't have to worry about a water clone catching her in a water prison because any of them that would rush her would be obvious and she would just throw shuriken at it.Not gonna lie u have some good points, but allow me to explain, eyyyy
1.He used it both the 1st fight and 2nd fight against kakashi, he used the 1st one to trick kakashi and got him in the water prison jutsu and used 10 of them on Sasuke, but Sasuke saw through it with his sharingan as stated in the anime and manga, i agree with u it isnt his always 1st move but he will use it against a skilled user such as Kakashi or Konan. If Zabuza is successful with his water clone diversion, he could trap Konan in his water prison jutsu and she wont be able to seperate out of there, causing her to eventually drown in Zabuzas own hand
2. She goes in the air, still not being able to see, then Zabuza can sight and strike her out with his water dragon jutsu which is an all range jutsu(which includes long), but will this probably damage her alot, no, but it will exaust her chakra as she is still flying in the air to avoid Zabuza and intangiling her body.
3. The chakram wouldnt be able to clear the mist, Zabuza embeddes alot of chakra into the mist as Kakashi stated "Hes building up a huge amount of chakra in episode 7, so the chakram maybe perhaps could move some away making some visibly by 10-20%. On top of that, Zabuza if he has to can embed more into the mist.
Im stating facts here
2. Since Konan is already in the air, she's using Dance of the Shikigami, so she wouldn't be hit, but if some stray papers were to be hit she is somewhat resistant to water so again, it wouldn't really do much as you said. Again with the whole Konan has more than enough chakra so flying wouldn't hinder her. :3
3. If Zabuza is determined to keep the mist up while Konan is throwing Paper Chakram, he could do it I suppose. But he'd be wasting more than needed chakra and by the time the mist is just unbeatable, his stamina would be drained a considerable amount hindering his performance while Konan is still fine.