We just saw Yuu lying to Hikari
His only real lie to Hikari was the dead phone thing. His real sin is the important information he ommited deliberately, or if you prefer, by cowardice and fear.
using underhanded methods to probe her reactions
This never happened, except if you are talking about how Yuu asks for Hikari during the dance in chapters 36-38 all those times why she is upset, trying to probe if she saw something, and even if it is true, this make Hikari into a liar too, who deliberately lied when she basically said Yuu she didn´t see nothing.
All this is not bad neither uncorrect, he is sincere, but he is not honest either.
hiding his relationship with Yami from everyone
Fuck? This never happened. Again, I don´t believe he hidded his relationship with Yami from everyone, and even more important, he couldn´t do it even if he really would try to do it.
His parents securely noticed the changes of him and forced him to reveal his relationship with Yami. They would be very bad parents if Yuu could change so drastically and never noticed nothing, I mean, even Hikari realized Yuu had an ex-girlfriend in somewhere after seeing him with Seki. The bother of Hikari is not Yuu having an ex-girlfriend, is that ex-girlfriend being her own best friend.
Again, there is a reason why we don´t have his Point of View yet... is definitely much more probably his parents forced him to talk about Yami sooner than later, and keeped the secret for him, like they never said nothing to Hikari about the failed exam of Yuu in her school, as Yuu omake chapters confirmed it.
The plot of Yami-Yuu relationship works much better if he really never tried to hid it and the only reason why Hikari never learned about it, is simply because Hikari was too naive an ingenuous to see it -and again, her thoughts in novel chapter 21 during the betrayal left very clear she was almost secure Yuu had an ex-girlfriend and that girl probably was a student of her school, and this is why Yuu didn´t want go to the cultural festival of Hikari school-
And of course, remember, all the plot of the first Hikari chapters is about she doesn´t know really to Yuu and they start the series more as neighbours than as real friends. This is the meaning behind plots like Seki, for example. Yuu has his own life and he doesn´t have to tell Hikari about it, and Hikari has her own life too and definitely unawarely ommited decisive information could have helped Yuu to identify that "Aya-chan" was Yami.
The only thing we know until now with relative certainty he lied to his family it´s about him having sex with Yami. And considering the legal consequences, again, Japanese laws forbide minors to go to a hotel and Yuu and Yami could have ended even in jail for their actions.
And yes, IMO if my theory is true, Yuu was lectured by his own parents after the beach hotel called them to say his son was fucking with his girlfriend and this is one of the reasons why he correctly suspects Yami family could be the real reason behind the ghosting.
being weak-willed and passive - and you really intend to argue that he is more of a goody two-shoes than Hikari?
I mean, Hikari is weak-willed and passive too, if not, all this fuck-up never would have happened in first place. Only a passive and weak-willed girl would stay passively in the door seeing how Yami slaps and later kiss his best childhood friend and actual crush without do nothing and crying as a shoujo fragile maiden.
Is this mutual passive personality from both Yuu and Hikari, the reason why the two were the perfect victims for a dominant girl like Yami.
Doing the right thing again, yeah. She wants the truth and doesn't want her love life to be full of lies.
This "virtuous" moment is not virtuous anymore, when she attacked physically Yuu and launched him to the floor. Not, that is not a right thing moment, is an abuse moment from part of Hikari even if she has good reasons to be upset with the half truths and convenient omissions of Yuu.
A perfect virtuous girl never, never, never, would have used the violence, even more after seeing the toxic ex-girlfriend of Yuu slapping him -so, a perfect virtuous empathetic girl definitely would have thought this previous abuse is one of the reasons of Yuu liar and suspicious actions-
You think someone like Kaoruko Wagari from Kaoru Hana ever would have do something like that?