To me, it seemed like it was strongly alluded that they were dead, very possibly killed by Ghetsis with the same move he tries to take out the BW2 protagonist with (Glaciate). Bianca and Cheren's contrasting dialogue in regards to the BW protagonist seems to imply this as well. Bianca is optimistic, constantly comparing the BW2 protag to the BW protag throughout the game and recalling up memories about them (such as the first step onto route 1. Cheren on the other hand appears to be more aware of what might have happened to the BW protagonist, rarely (if ever?) mentioning them until things get dire. And when he does mention them (upon the realization that one of the Heroes is needed to defeat Team Plasma) it's in clear frustration (and possible grief). He questions where the Heroes are, why they are away when they're needed, why they aren't living up to the responsibilities placed on them, etc. before vowing to find one of them. It is off course N who returns, and not Touya/Touko. Maybe it's this contrast between Cheren and Bianca's outlooks on the protagonist's fate that caused them not to speak to each other for two years (as mentioned early in BW2). Cheren, rooted in reality, couldn't bear Bianca's naive optimism. The mother of the BW protag also has the same general demeanor about the missing protagonist as Cheren, desperately hopeful the moment the BW2 protag appears in her house but immediately after falling into a manner that is more grim acceptance than anything. Assuming Touya/Touko went after N like the mother says, it's highly possible they ran into Ghetsis first (plus, Looker had more or less placed task capturing Ghetsis and the sages on the protag's shoulders, yes?). Perhaps the protagonist was unprepared, and more than likely they were alone, cornered in a dark place with Ghetsis and Kyurem with no way out.
TL;DR - they're dead
