Dear Sally, we use corning costar 3599 F-bottom 96-well plates with lid to determine bacterial growth in microplate reader with incubation. Another way, as Khilood suggestion, to use sealing foil some of them breathable. Axygen (Corning) produce sterile breathable sealing foil. Breathable films allow effective gas exchange for cellular/bacterial cultivation while preventing contamination.
An other option is letting the plates come to room temperature before your measurement. The condensation will clear off eventually. However, you may not want to have your cells sit out at room temperature for too long, especially if you are using a buffering system that depends on CO2.
In my opinion to remove lid can lead to both contamination of 96-well plate and microplate reader. You should use lid or sealing foil, because, it takes o/n or 24 h incubation without removing plate from microplate reader.
There are a lot of options for gas permeable seals - we've had success with mammalian cell culture, but I'm assuming they could also be used for bacteriological work.