Are you taking her to pet stores for the experience or because you have shopping to do?
Are you giving her a chance to potty ahead of time?
What I would do is take her to the store after she's gone to the park (or gone for a walk) so you know her bladder is empty (or mostly empty). Whenever I take my dog into a store, we always potty ahead of time. I try to avoid that one area right outside the store where ALL of the dogs go and take my dog to the perimeter of the parking lot to potty. This way, my dog doesn't associate going to stores with marking.
Then, walk up and down the aisles rather quickly. Walk in the middle of the aisle. Don't let her sniff the goods, just cruise up and down the aisles. Most adult dogs don't have "accidents" in stores (meaning, they can't hold their bladders); as you realize they intentionally mark. Usually, they're marking a corner of an endcap or a post. So don't let her get near enough to one of these. Keep her moving. Take her to a variety of pet stores. Big box stores, I've noticed, tend to have more of these "marked" spots than smaller stores. This is probably because they're bigger, so more owners allow their dogs to roam at the end of flexi's relatively unsupervised.
Your task isn't for you to shop. It's to train Heidi that she can and will go into a store, walk around it, and come back out without marking in it. The quicker you can keep her moving in the middle of aisles, cruising throughout the store, so she has to pass the same spots over and over, the quicker she'll learn that she can (well, has to) pass marked spots. But in exchange, she gets to see the whole store, which is interesting, and she does so at a brisk pace, which is fun.
Don't bring her into a store when you're there to shop for now. It will probably take her several months of going to stores a couple times a week until she gets it, that she's not allowed to mark anymore.
There are times when it's ok to mark. If we're near a park or on a walk and passing the hydrant that I know ALL of the dogs mark, then I will give my dog the ok to mark. But marking (indoors, on plants, other people's property, etc) is a rude behavior, and yes, our adult dogs can control it.
But we have to train that, just like everything else.
I'm sure you can do that with a bit of consistency