To accurate model the orbits of the planets for a long period of time one must look beyond Newtonian physics to some extent. JPL uses a post-Newtonian correction to develop its planetary ephemerides. JPL may well employ a post-Newtonian correction for the paths of their interplanetary missions, but only because they already have this mechanism in place. (They almost certainly do not have it in place in the spacecraft flight software. If they do use a post-Newtonian correction, it would be in the best estimate of trajectory (BET) calculations performed after the fact.)
Those corrections are not truly needed for interplanetary missions. As Nabeshin mentioned, the errors in the sensors, effectors, and control algorithms on the spacecraft and in the errors in the external measurements used to anchor the spacecraft 's state will vastly overwhelm the tiny errors that result from ignoring relativistic effects. The time spans are too short, and except for missions to Mercury, the gravitational effects are too small, for GR to result in any noticeable deviation from Newtonian gravity.