Of those that view your auction items, few will look for a store link unless reminded. People will read your item description, but not look to see if you have a store. You should at least include, prominently, 'Visit my store for similar items' as part of the auction item description.
Here is an example of the problem you are having. Go to eBay and search for 'half pcgs ms69'. I found 13 items that match, but
>THIS (click here)< item was missed. That's because it's in a store.
The 'THIS (click here)' above is an example of the 'link' I mentioned. You don't really need the link part, but be sure to at least mention your store as part of the description in a regular auction.