I have never had any issues with my gobies hanging out under my clams. In fact, a lot of fish like to hang out under there from time to time.
Having said that, some clams are a lot more sensitive than others and those ones will tend to close up frequently whenever they are contacted. You kinda have to just keep an eye on that. If the clam remains wide open while the goby is hanging out underneath temporarily then I wouldn't worry about it.
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