There were quite a few more than just two on my visit (August last year) so there should still be a few left, although not sure exactly how many. I doubt they do plan to phase the species out, as a major new orangutan enclosure, 'Sumatra Regenwald,' is planned for an unspecified time after 2031, although given how long the wait for it may potentially be, and how poor the current housing is, temporarily moving away from apes may not be the worst idea. The gorillas, who have a similarly poor enclosure elsewhere within the Affenhaus, will thankfully be receiving an improved enclosure much sooner ('Kongo,' opening in 2029), although even still, for whatever reason, the zoo is prioritising renovations to their already-excellent big cat exhibits and the Pantanal complex, as well as the construction of a cable car ride.
This article on Zurich's website explains in good detail what their plans for the future are.