But it is hinted at long before. After the accident (1999; Jodie is 9) there are only 4 scenes in the timeline where you see Nathan before Jodie is taken to the CIA. The first is The Party (2004; Jodie is 14), where he only appears for 1 minute and obviously hasn't been destroyed yet by his grief. He recovered and appears rather normal because Jodie is giving him a purpose and keeps him busy. Next up is Like Other Girls (2006; Jodie is 16), where Nathan has already developed a deep relationship with Jodie and cares for her. The Condenser (still 2006) follows and it is confirmed in this scene that this is the first time the DPA has ever build a condenser. So what Nathan plans at the end of the game wasn't possible before this day, so he obviously couldn't think about it prior to this scene. At the end of the scene where Jodie warns him to never build another condenser ever again his facial expressions are those of a conflicted man and give away that he already developed thoughts in bringing his family back. This is the first hint. The final scene is Separation (2007; Jodie is 17) where the game pretty much reveals to you for the first time that his daughter died while Jodie has the flashback through the music box. Nathan is acting weird when Jodie tells him about it. The mere fact that he put the music box there fully knowing what Jodie would see already shows that he is getting obsessed over seeing/hearing about his family. You can ask Cole about it and Jodie says "Don't you think Nathan is acting kinda strange lately?" and he replies "He is probably just nervous because he tries very hard to raise money for the lab at the moment". This is the next hint. He is acting strange and tries to raise more money for his research. Obviously it gets even worse when Jodie is taken away from him, the last person he really cared about that kept his attention elsewhere and saved him from going mad.
He is finally receiving all the funds he needs after he turns to the military for help (by promising them military applications in return). This is revealed in the Old Friends chapter. Granted you never see this happening because it happens while Jodie is working for the CIA. Nathan is promoted to the head of the DPA which builds another condenser closely under his watch. Between Separation and Norah (where Jodie finally sees Nathan again) almost 8 years have passed (2007-2014). So you don't know what happened to Nathan or what he did for almost 8 years. This long period of time is enough for his insanity to grow, especially since he is without Jodie and now knows about the condenser technology.
When Jodie meets him again during Norah he is already acting very strange towards her and she grows more and more suspicious of him. You can even fly with Aiden through the wall and already see the machine he build to communicate with his family. Finally during Black Sun it escalates when Jodie allows him to talk to his wife again for the first time since 15 years. He goes mad and basically interprets "let us go" as "release us into the real world". He is not really evil, he does what he does in good faith despite being insane.
So yeah the way Nathan is presented makes sense and there is no plot hole when you look at the whole timeline. However, I do agree with you that it could have been better presented to the audience. It all comes rather quick to have a tense finale without a proper build-up. But this has more to do with the execution and not with the way Nathan is written.
I didn't really mind it, because I saw it coming a long time ago. The hint during The Condenser chapter combined with Separation was enough to make me aware that something is very wrong with him. Some other LPers also figured this out around this point e.g. Jesse Cox. It isn't difficult if you pay close attention. Also Dafoe does a pretty good job carrying it through his facial expressions.
EDIT: Attached timeline for reference (click to enlarge):