It's possible the cortical node is integrated into the brain, but doesn't remove any of the said tissue, merely makes room for it by pushing it aside.
Or, even if it does eliminate a portion of the brain, then the Doctor would likely be able to regrow it via stem cells or other forms of therapy that were developed.
Keep in mind that they are centuries ahead of us in terms of medical capabilities.
It wasn't until the Vidiians showed up that they started to dumb things down for them.
Plus, with the arrival of 7 of 9, a lot of the problems were treated using her nanoprobes (even in cases when Fed tech was more than capable of doing the same thing).
Plus, were any of the away teams body parts amputated?
I don't think so.
regrowing new eyes or body parts would be simple for the Doctor.
Plus, 7 of 9 was a special case.
She was a Borg for 18 years, thus her body became too reliant on some of the Borg technology which couldn't have been removed (such as the Cortical node - which doesn't mean they wouldn't be able to find a way to do it later on).
A person can be assimilated for a certain amount of time before their body becomes too reliant on Borg technology... if this time frame is not exceeded, then removing said technology and making the person 'as new' would likely be simple.
I was surprised though in Ds9 that Nog had an artificial leg.
Seriously... for their level of technology, Nog should have had a completely new organic leg.
But again, Ds9 tried to make things look 'realistic' so they dumbed down technical capabilities.
What idiots.
Voyager was at least 'realistic to the Trek universe' most of the time.