Yea, actually, I did find those darn Sand People rather irritating.
While Tatooine and Kashyyyk are Czerka controlled, and they are allied with the Sith, there still is no Sith military presence on either planet. Consider the fact that the Leviathan is the flagship of the Sith fleet with two very high-value targets on it, making it very vulnerable to be completely alone. To send the Leviathan to Tatooine or Kashyyyk would mean it would have no forces on standby to help it if it were to come under another Republic strike similar to Bastila's strike on Revan's ship. I think the only way the Leviathan can safely travel is within, or close to, a Sith fleet presence, such as in the Manaan system. Even if the Leviathan were to be escorted to Tatooine or Kashyyyk, the Republic could still be desperate enough to mount a strike. I don't see Malak taking the chance.
Manaan just seems like the safest place for the Leviathan to abduct the Ebon Hawk, to me. It can remain relatively isolated, rip the Hawk out of hyperspace, and not need to fear Republic fleet intervention because the Republic wouldn't dare try anything even remotely near the Manaan system.