From what I've heard, the "-kun" suffix is somewhere inbetween "-san" and dropping the whole suffix thing altogether, and yes, it is a sense of formality between people. And here's a bit of extra information: the "-chan" suffix is an even more informal way of adressing someone very close, like a best friend [mainly a female]. I'm not just saying any person here because people find it rude to address people you're not close with using that honorifc. Calling someone "-chan" is the exact same thing as giving someone a nickname/shortened version of their name.
Also, dropping any suffix doesn't always mean you're close with a person. Notice how Sasuke himself doesn't use honorifics for anyone, because he refuses to address anyone in a polite manner. People would consider that rude/insulting.
Anyway, I think the whole "Sakura is still addressing Sasuke as Sasuke-kun" thing would just a habit by now. I think that some [pfff most

] of the NH fandom that also ship SS misunderstand the whole suffix thing and the "OMFG SHE STILL CALLS HIM SASUKE-KUN!!11!" thing a little too far.
Yeah, I don't really think this whole suffix thing is a viable argument for or against any pairings. The "its just a habit" part, I don't think applies only to Sakura. I think it goes for everyone in the entire series. For example, Hinata still adresses Kiba and Shino as "Kiba-kun" and "Shino-kun" respectively and they are on the same team together. However, Kiba has always referred to Hinata as simply "Hinata". Why? Well because Hinata and Kiba are very different in terms of personality. Kiba is loud, brash and overall doesn't seem to have a lot of respect towards authorities. Hinata, on the other hand, is shy, introvert and seems very concerned about proper etiquette, which probably has something to do with her upbringing. Also, none of the members of Team 10 has ever adressed eachother as "-kun" or "-san". Why? My guess is because they seem to have very strong clan relations, especially through their fathers, so they've probably had a lot of time to get acquainted even before the series began, at least in Shikamaru and Choji's case. And what about Naruto? To my recollection he has never adressed anyone in the K11 (other than Sakura) with a honorific, because he is very much like Kiba. Loud, brash and doesn't have a lot of respect towards authorities or social norms.
I could go on all day, but my point is that it all comes down to things like upbringing, personality and what bonds certain characters may have had (or not had) prior to the series start. With that being said, even If we were to compare say, NaruHina and NaruSaku in terms of honorifics, I think that NS would win, because even though Naruto adresses Sakura with "-chan", from your post I understand that "-chan" is sort of an exception and that instead of denoting formality it actually denotes closeness and affection. Also if adressing someone without a suffix means that you are close to that person, that means that Sakura adressing Naruto as simply "Naruto" at the very least means that the two are very close (either as friends or lovers, your choice

). Similarly this can also be applied to Naruto simply referring to Hinata as "Hinata". Meanwhile, Hinata has always referred to Naruto as "Naruto-kun", which means that even though she respects him and wishes to be closer to him she still distances herself from him by using that particular suffix. So basically, NS has one affectionate suffix and NH has one slighty formal suffix. It still gets a bit sketchy though, as once again it all comes down to personality and upbringing. Hinata is just polite. Naruto calling Sakura "Sakura-chan" simply comes from when he still had a shallow crush on her (i.e. when he didn't know her all that well, but still liked her regardless) and Sakura refusing to call Naruto with any suffix was originally a sign of disrespect towards him. So yeah, in the end it's all completely pointless IMO, just like my entire post.
As for the whole acknowledgement argument, it doesn't really matter whether Hinata was the first to acknowledge Naruto or if she respected him when noone else did. Like some of you already mentioned, in the end none of it made ANY difference whatsoever on Naruto's part. He was still all alone and was hated by pretty much everyone. He desperately needed someone, anyone to acknowledge his existence. But she never did. All she did was stand behind trees and whatnot, watching him. Sure, she may have been too shy, but if at the point she truly knew Naruto as well as some people claim, wouldn't she have known that that is exactly what Naruto's philosophy is about. Helping and protecting the ones you care about, no matter what. So, what she should have done was to reach out to Naruto and thereby overcome her shyness in order to help someone why desperately needed it. This may sound like im bashing Hinata, but im not. Im simply adressing a part of Hinata's character that, while not all that flattering, is still an integral part of what makes her who she is. Just like one of Sakura's worst traits is her emotions and how she often lets them control her, Hinata's worst trait is by far her shyness and her inability to muster up the courage to help those she cares about. This is, however a trait that she has slowly learned to overcome over the course of the series, like when she jumped in front of Pain to protect Naruto. In fact that was the culmination of most of her character development, i.e. overcoming her shyness (telling Naruto about her feelings for him) and helping someone precious to her (Protecting Naruto from Pain). The only loose end now is for her to know whether Naruto shares her feelings or not. Whether Kishimoto chooses to tie up this loose end remains to be seen. Meanwhile, Sakura has yet to overcome her greatest weakness, i.e. her emotional turmoil and her confidence issues. However the way I see it, Sakura's emotional problems are a bit more complicated than Hinata's. For one, Hinata's emotional turmoil pretty much boiled down to not being able to tell a boy that she was in love with him, while Sakura had an unrequited love for a boy(Sasuke), who besides not sharing her feelings also used to belittle her and call her annoying. Then said boy left the village and later on became a wanted criminal. A criminal that she suddenly had to kill while trying to protect the feelings of another boy (Naruto) who, unlike the first boy, always encouraged her and alwasy were there for her, but who also saw the first boy as a brother. A brother that he wanted to save, not matter what. Meanwhile, she is confused and maybe ashamed about her feelings for the first boy and she may even begin to develope romantic feelings for the second boy, all the while feeling inferior to both. So basically Sakura is currently trapped in a really f**cked up love triangle.
As for her confidence issues, well I've already covered that in anther thread somewhere, but it basically boils down her doubting whether she truly will be able to surpass her master (Tsunade) in light of her recent "failures", such as not being able to kill Sasuke and realizing that she can't really do anything to help Sasuke or Naruto with overcoming their plights.