Duik controllers may be standard After Effects shape layers, with a bunch of expressions and a simple effect to control them. The controller appearance is controlled by this effect and expressions, and this reduces the performance, to the point it can be a big issue in complex projects.
Baking* the selected controllers removes all these expressions (and deactivates any dynamic display) to improve the performance.
Hidden controllers, even if they’re not baked, should not have a big impact on performance.
▷ Read the Advanced / Performance section for more tips about how to improve performance in After Effects and using Duik.