I think a lot of this is working of modern prison assumptions. Plenty of prisons in SR are for profit private facilities. Unless something pays off in the long run, they are not going to invest money into it. This means that unless it's really simple to remove or disable, they are not going to bother with it and instead just throw the guy into a hole in the ground. Trampling a persons rights is a lot cheaper than making him fit for staying with the general population, especially when that someone is a SINles. This even applies for the non private prisons.
As far as physical improvements go, I'd think a prison would be build with those in mind, so none cares for your muscle replacement. You'll simply be assigned appropriate work duty. Comlinks get likely removed as well on top of jammed.They probably remove cyberlimbs as Firebug said and are likely to remove the blades and such from spurs etc. since it's easy to do. Other cyber weapons, move-by-wire, heavy duty wired reflexes or other stuff that turns people into walking weapons simply get thrown in solitary with no contact to the world whatsoever.
I'd also like to point out that being SINles in a corporate for profit prison is about the worst possible place in the world. The corps need to test all those new drugs, implants, nerve agents, vaccines, bio weapons etc. on *someone*. Guess who volunteered by getting caught. And if you're trouble? Well, none is going to check whether or not you're serving your time alive or dead. Legally, you don't exist anyway.