Yes, both are possible. I am not sure if we have this store here. ~ I don't really know whether or not we have this store here (maybe we do; maybe we don't).
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AnonymousThanks. So for the second one, do I need to use the word 'that'?It is not mandatory, but it's probably better to include it in careful formal writing. It is often omitted in speech.
AnonymousAnd, basically the second one suggests that, as you explained, I am quite sure that we don't have the store. Did I understand correctly?