Premier League West Bromwich Albion have run the rule over the pair, who both were given their chance in the latter half of the season.
Striker Johnson, 21, was signed by County from non-league Nostell Miners Welfare last October and scored six goals in eight starts for Jim Gannon's side.
Johnson has also been linked with a possible move to Fulham.
Central defender Thompson, 18, came through County's Centre of Excellence having been spotted by development manager Alan Lord, who left the club last week at the same time that Gannon and his assistant Peter Ward were made redundant by administrators Leonard Curtis.
Tommy Rowe was sold to promoted Peterborough earlier this week as the administrators looked to raise funds to pay wages of those still at the club.
His younger brother Danny, who made his debut at the end of last season, has been targeted by both Liverpool and Celtic.
County's Centre of Excellence, which helped produce a number of current Stockport players, has survived the cull.
Compensation
Youth team manager Craig Madden will be staying on, along with Centre of Excellence manager Mick Wiblin.
Wiblin said: "I had been told that the youth set-up was being shut down, but after the club went into administration I was asked to stay on, along with Craig Madden, and get the Centre of Excellence back up and running.
"We could have lost a lot of young players for nothing to predator clubs if the Centre of Excellence had closed down.
"However, I have been told by the League that we still have our academy licence so if a player was to move now, the club would receive monetary compensation.
"I was amazed that the manager or the board, or whoever took the decision, made it, because the Centre of Excellence has been very successful.
"But, as far as I know, everything is back to normal, and the lads who have been offered youth contacts for next season will have those honoured."
Administrators Leonard Curtis added: "We can confirm that there are no current plans to discontinue the Stockport County youth facility, including both the Centre of Excellence and the youth programme.
"The administrators have identified these facilities to be of value to the club."
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Showing comments 1 to 8 and replies | View All
bru50, stockport (14/05/2009 at 10:39)
Are Rowe, Johnson and Thompson not of value to the club then?
Todd, heywood (14/05/2009 at 11:08)
The unpalatable truth, Manchester (14/05/2009 at 12:39)
Mullet Vision (14/05/2009 at 12:53)
Todd, heywood (14/05/2009 at 15:03)
bru50, stockport (15/05/2009 at 12:32)
.....................and we still haven't won anything since, or been to the new Wembley and won!!!!!!!!!!
Maybe this is the unpalatable truth!!!!!!!!!
Clive Farrington (18/05/2009 at 09:50)
Ken Adams, Stockport (19/05/2009 at 13:36)
Or two poor ones and be in the Conference. Mine seems more realistic.