You can certainly leave the bins empty, or you could use them for storage of small items like clean water bowls, hides, paper, etc. Also having a spare bin clean and empty tub available is convenient when your snake spreads crap all over the plastic of its current bin.
I would not advise leaving the slot containing the thermostat probe empty with no bin in it, as there will be more air exchange in that particular opening compared to the others, which could cause the openings with bins to run too hot.
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