Wasn't there a level in game where you had to find a generator or something and turn the power back on in the mall? Ellie and her friend ride the merry go round.
I would guess that wide shot is CGI (or at least what they call digital set extension -- shooting on a live set and using CGI to make it look much bigger), and they shot the close action shots in the actual mall.
As for what stores can be seen, that would depend entirely upon which stores gave them permission to use their logos in the show (or in some cases, paid to be included). They would have either used false fronts on the stores or digital replacement for the signs.
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