Im about to run my projector to test how hot it gets. Will it be ok if I subsitute the lcd panel with a sheet of wood so I dont damage the lcd panel while testing, or will the temperature reading be higher since the light rays arent passing throught the projector?

What are you measuring the temperature of?

If you are trying to measure the temperature of the LCD, then I think replacing it with a bit of wood, would indeed give you a higher reading than usual, but probably not significantly so.

If you are measuring the temperature of the air going through the projector, then I suspect the difference will be negligible.