The Shadowrun subreddit had a worldbuilding thread in the last couple months that dealt with prisons. You can start looking there.
Throwing in my 2 nuyen, when it comes to managing Awakened prisoners, I really don't like the draconian nature and limited usefulness of things like mage masks and mage cuffs. In my game there's a chemical solution to that problem that suppresses peoples' connection to magic. A newly processed prisoner would receive injections every couple of hours, and over the course of a day their connection to magic would go away completely. Then the prisoner could join the general population. Much cheaper, humane, and feasible than canon methods. The doses taper off to once a day, then once a week to maintain the suppression, and Magic returns at a rate of 1/day once the doses have elapsed. This opens up RP opportunities to infiltrate and replace the drug with saline or do some social engineering on the medical techs. If the poor sod is in the clink for years, they may suffer permanent damage to their Magic. Old ex-cons may have lost their talent for good.