In TV canon, they never explicitly state the doctor has removed all trace of the Borg implants.
But it can be inferred that eventually the doctor removes all the Borg implants (or as much as Federation science allows). As the assimilated crew did not develop relying on those implants as Seven did their natural systems were able to take over all body functions with assistance from the Doctor. Looking at Picard, after his assimilation and rescue, borg implants remained. Those implants were reactivated in First Contact to allow the Borg Queen limited access to Picard. In Endgame both Janeway's are examined and there is no mention of Borg implants in their comparison. We discover that Adm. Janeway does have a piece of modified Borg technology that allows for direct mental interface with computers. She uses that to communicate with the Queen, but if she had the level of remaining implants that Picard did she wouldn't need it.
Multiple times the Doctor is shown to have a far better grasp of Borg implants than the Federation as the series progresses. It is also revealed in Human Error (s7e18) it is possible for Seven to remove more of her implants with extensive (and hazardous) surgery, but she does not actually embark on them until Endgame (s7e25) in response to her relationship with Chakotay.
With the ability to remove any implants that don't effect biological function, and eventually the ability to remove those that do, leaving the implants in longer then absolutely necessary would constitute a liability both in the health of the crewmember, and when facing the Borg (as it was for Picard in First Contact).
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