If I use only one of the PECL differential outputs and the unused output is terminated in 50Ω, how will this affect the phase noise or jitter of the single-ended output?

The output signal swing is now halved. This can have phase noise or jitter implications for the receiving circuitry. It is important to note that the rise/fall time of the single-ended PECL output are not equivalent; generally the rise time is much smaller than the fall time. If the receiving circuit uses the single-ended falling edge for critical timing this may be a problem.