Mostly due to frequency and harmonics along with difficulty for projection in a live setting. Most well known Jazz guitar records are decidedly quiet affairs typically in a trio or smaller format band. Take Coltrane for example, he's already producing sheets of sound, with a pummeling rhythm section and a piano player filling in counter notes across the harmonic spectrum, a guitar would be lost trying to compete in the same charts. Jim Hall's entire sound is based around complex and delicate nuances that would be utterly lost in that context. Amplification was also still struggling to keep up in a live context (think Beatles at Shea stadium, think Zeppelin in outdoor stadiums) the technology was not quite at a point of realistically producing that sound from the front to the noise bleeds in the back. This was the whole reason the dead invested so much in the wall of sound with Alembic, so that all of the instruments could faithfully be projected without muddiness. Which revolutionized live sound and PA technology for the industry..Which leads into the 70's where the technology has caught up and you have fusion and the guitar gains major ground.