I think the only way for it to ever end a franchise is for a title to sell so horribly that it buries any chances at a future sequel. And any developers would shy away from ever attempting to revive a failed franchise. But Zelda has been such a top selling franchise for so long it might take a few bad games to come even close to that. Even then, a few bad reviewed games has not stopped the Sonic the Hedgehog franchise at all.
I do not believe that the developers are at all concerned with ending a timeline and by extension the series by answering mystery questions in the game's story. There are already a few Zelda games, such as the oracles or FSA, that do not fit into any timeline at all but they are still fun to play. And nintendo does not appear to be nearly as concerned as the fans are with making all the little ends meet perfectly. They are more interested in making the games and then adding the extra flavor in the story later. Even after that all these games are moving backward, so what if we know who the interlopers are or where the master sword came from. They can always do what everyone else does, move forward. Perhaps someone else could try stealing the triforce for themselves, it is a tempting item for any would be conqueror, while Hyrule is within a fantasy world so there could be many other adventures to be had outside of the same old Ganon kidnapped princess routine. ST introduced a demon race that existed before the Hylians, the Twili have shown that there are other tribes that are not as friendly as those found in Hyrule, and MC and FSA have shown that magical items found in Hyrule can corrupt others towards villainy. In a setting like Hyrule I do not see how the story could ever possibly end.