No, a moderate body lift will not affect those things. The maximum recommended body lift is about 1.25”. There is also a 3” option, but it requires modification of the fuel filler neck, fan shroud, and other items, it has questionable mechanical integrity, and just looks awful.
On the note of mechanical integrity, if you do install a body lift, avoid anything that is made of a compressible material (such as made by JKS) - those do not support the body well and will damage the body over time. The recommended option is aluminum spacers.
Two more notes on body lifts:
1) The radiator fan shroud is connected to the body. When lifted, the shroud will no longer surround the fan correctly and will be chewed up by the fan. You can either easily drill new holes in the plastic shroud to re-center it around the fan, or install a motor mount lift.
2) A motor mount lift not only will tilt the nose of the engine upwards so that the fan and shroud play nice again, but it will also change the slope of the whole drivetrain so that the rear transfer case output flange/shaft is pointing more downward. This can be helpful to avoid excessive driveshaft operating angles if the suspension is ever lifted or if the transfer case is ever tucked up higher for more ground clearance. Because the rear driveshaft of a TJ is so short, driveshaft angles (and driveline vibrations when angles are excessive) are a real battle when changing the relationship between the transfer case output and the rear axle yoke.