Midfield dynamo Lee, 30, and centre-forward Hooper, 30, are running again following long injury lay-offs.
But Agnew, who was in the dug-out for the first time on Saturday as the Owls were held to a goalless draw in the FA Cup by League One promotion-chasers Luton Town, is refusing to put a timescale on when Lee and Hooper will next be available for selection.
Agnew, holding the fort until manager Steve Bruce officially starts his job on February 1, said: "I think it is early (in their recovery). I don't really know the depth of their rehab and where they are at with it all and when they are going to start playing football again.
"They are certainly quite a while away."
Neither Lee nor Hooper have made a senior appearance for the Owls since December 2017.
Lee, a key figure in the Wednesday side that reached the Championship Play-Off Final nearly three years ago, has been troubled by hip and recently knee problems.
As for Hooper, who bagged 11 goals last season, he underwent groin surgery last November.Â
Lee and Hooper are out of contract at the end of the season.