Thompson has an ankle problem while Close is wrestling with a thigh strain and both players are doubts for the match this weekend.
Gareth Evans, Brandon Haunstrup and Jack Whatmough will all miss out with knee injuries.
Milan Lalkovic (Achilles), Stuart O’Keefe (groin) and Danny Rose (leg) are also sidelined.
Scunthorpe’s new signings Ivan Toney, Ryan Yates and Cameron McGeehan are all poised to make their debuts.
Striker Toney (Newcastle), plus midfielders Yates (Nottingham Forest) and McGeehan (Barnsley) have all joined on loan until the end of the season.
Skipper Rory McArdle could return to contention after missing the last five matches due to a groin injury.
Midfielder Sam Mantom (groin) is three weeks away from a return to action, while Jonathan Margetts (knee) and Jordan Clarke remain long-term absentees.
Southend manager Chris Powell led the applause for Jason Demetriou after the right-back scored twice in the 3-1 win against Portsmouth at Roots Hall.
Morecambe boss Jim Bentley was the happier manager after Gregg Wylde's 90th-minute strike earned his side a point in their 1-1 draw with Forest Green.
Manager Gareth Ainsworth described Wycombe's 2-0 win at Cheltenham as a thoroughly professional performance.
Skipper Richard Wood scored the winner just before half time as in-form Rotherham pulled off a 1-0 victory at League One leaders Shrewsbury.
Accrington Stanley boss John Coleman was pleased with his side's second-half rally after they came from behind to draw 1-1 at gutsy Barnet.
Notts County manager Kevin Nolan thought his side were denied a stonewall penalty during their 0-0 draw with Newport.