Checkpoints are a DLC item that allow guards working on it to perform pat-down searches on prisoners and visitors who pass through it (Although searching visitors has no effect as contraband spawns from them inside Visitation). They may cause congestion and significantly slow down the speed at which prisoners travel.
Checkpoint will enforce all ten tiles it occupies to have one-way movement for prisoners. Unfortunately, as of the sunset update, all changes to one-way movement within deployment will be reverted back to it's default state within one 24-hour period. It is important to note that only the directions channeling into the guard are enforced. If a custom prison set up two checkpoints for two-way movement, it is possible to snake through both of them taking the opposed direction during escape mode and free of body search.
Prisoners don't like being searched, so similarly to the metal detectors, they will avoid going through them by picking another way around (if possible), especially if they carry contraband.
The efficiency of pat-down searches depends on the tiredness of the guard performing them so having them well-rested is important.