Well, in the original Naruto story, there are strong themes of hope and redemption. However, in 'Naruto becomes dark yaoi fanfiction', these themes can be drastically altered. Naruto becoming dark means that the hope he represents in the original might be lost. And the yaoi elements introduce a different kind of relationship dynamic that wasn't present in the original. This can make the story more about these new, often darker and more controversial relationship aspects rather than the positive themes of the original Naruto story like the power of hard work and the importance of family and friends.
The original Naruto has themes like loyalty and the pursuit of dreams. In the 'Naruto becomes dark yaoi fanfiction', these themes can get muddled. For instance, if Naruto's character is made to be dark and involved in yaoi relationships, his loyalty to his friends might be re - interpreted in a more complex and sometimes negative way. Also, his pursuit of being Hokage could be sidelined as the new, darker plotlines take over.