We also use lids here. We find it easier to contol humidity like that. Given we only use hovabators... If we were using some of the more professional style incubators where you can set the humidity levels... then things may be different.
Definitley use lids. I incubate with completely sealed containers and a 1 part vermiculite to .8 parts water ratio by weight, and open the sealed container every 1-2 weeks for air exchange.