It might. My terrarium runs warmer now than it did before I had the top covered, but I also covered and insulated the sides so it was a pretty dramatic difference for me. You may need to adjust the thermostat down a degree or three, but other than that I wouldn't worry about it.
If you have it set up so that the termostat probe is between the glass and the uth and the thermometer probe is in the cage, on the glass over the uth, then it only makes sense that there will be a bit of a temperature discrepancy. The thermostat probe will not be affected by the increased air temp because it's not in the cage. The thermometer probe will. But that's why you need both, because the temps outside the tank are just as important as the temps inside.
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