Cyberware scanners (p. 334, SR4A) to detect cyberware. Containment manacles (p. 335, SR4A, under Restraints) can keep implanted weapons sheathed. Maybe there's a dedicated "computer technician" on prison staff specifically to hack cyberware to keep "combat mods" turned down/off--you don't need wireless to do this, just piggybacking the normal maintenance procedure will do, and some tougher jurisdictions may do this as a standard booking procedure (scan for 'ware, then plug in and deactivate what they find).
Bioware and genemods are more problematic, since they don't come with an off switch and they're generally less obvious to scanners (if detectable at all). But then, how do we control the stronger prisoners now?
Two other options for longer-term prisoners (like prison sentences as opposed to holding cells): solitary confinement or removal of the offending 'ware (which probably happens anyway for restricted or forbidden cyberware, since the convict no longer has a license for it).