QPR defender Steven Caulker is to undergo a medical at Southampton on Wednesday ahead of a season-long loan move.
Brentford midfielder Jonathan Douglas has been told his time at the club is over by new boss Marinus Dijkhuizen.
Midfielder Hughes, who joined Aberdeen last January, has agreed a new 18-month deal, while full-back Naysmith has extended his contract until the end of the season.
Both players have established themselves as key players in Craig Brown's plans and the Dons boss is delighted to secure the experienced duo.
"Both players are happy to be at the club and we are happy to have them," said Brown.
Hughes is likewise happy to have penned a new deal until the end of next season.
"It is good to get the contract done," admitted Hughes. "I have a bit of security now and I feel there are good times ahead here."