When long-awaited drawings of the new plan to rebuild David Geffen Hall, the New York Philharmonic’s home at Lincoln Center, were released earlier this month, James Kennerley’s eyes were immediately drawn to the blank wall above the stage.

He was looking for pipes.

“I was surprised to see there was no pipe organ case,” said Mr. Kennerley, the dean of the New York City chapter of the American Guild of Organists.

Organists, and those who love the natural, visceral sound of mighty pipe organs, have long lamented that both of New York’s premier concert halls, Carnegie Hall and Geffen, got rid of their old pipe organs decades ago and went electric. They see the coming renovation of Geffen as a chance to right a historical wrong, especially at a time when many of the world’s most glamorous new halls — including Walt Disney Concert Hall in Los Angeles, the Philharmonie in Paris and the Elbphilharmonie in Hamburg — have installed mammoth new pipe organs.

But the Philharmonic and Lincoln Center must weigh the desires of organ aficionados against other competing needs. For money, of course, but also for an even more precious New York commodity: space. How much square footage can or should be devoted to an organ, which plays a key role in a beloved but limited slice of the core orchestral repertoire? And the hall’s planners face a classic renovators’ conundrum: Do you go with built-in, or something more flexible? There are pros and cons to a new pipe organ, as well as to one of the latest digital models, which boast ever more realistic samples and better sound technology.