I would argue that they will have a hard time when freed.

The mind will refuse to accept that everything you thought to know about you, your history and reality is a lie. This will eventually pass and the mind will let go.

Physical symptoms will be over-stimulation, because they never used their eyes before for instance.

The muscles are atrophied, so they will have to be rebuild again via electro-stimulation.

It seems to me that the physical difficulties are only temporary. The freed people will be fully capable to have normal lives, sire children and even to go to war.

Permanent damages might include psychological problems like insomnia (because they already slept a great proportion of their lives) and some kind of Stockholm syndrome where you would prefer to go back into the Matrix than living in the real world. I find it very likely that the situation in Zion is very depressing to a freed mind, in a clinical sense.

Anyway, an advantage of the "pod-born" to the natural born people of Zion is that they can jack in and out of the Matrix or any other program in the construct. Plus, it takes a very resilient mind to see through the illusion of the Matrix, make the subconscious choice to go out of it, and survive the trauma of getting freed. The resistance seems to do a pretty good job in picking the right applicants for the red pill.

I am Sophophilie, thank you for coming to my TED talk.