Depends on which ones. If you get the lightsaber one or some of the costume ones (those two linked to finding holocrons) then it removes the holocron for each in the levels, which in turn would prevent you from obtaining the achievement for collecting them all. Or so I would assume. Also I would guess that using the cheats to increase your character's level would do the same thing, as that is the case with all over games I've come across.
However if you want to play as Proxy or Koda, then those cheats shouldn't change anything.
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