What an idiot. I took a bite of my own bait.
I just went through nearly all of the Home Depot stores in SOCAL. (didn't take that long actually)
The You Tool hardware store is NOT based on any of them, or at least not on any particular one.
Some of the design, colours & overall appearance are a loose match though.
This store in Palmdale is one of the best matches, & it's not even close.
The same design principle probably applies to the strip mall on Route 68. (and a couple other places in the game)
The Dollar Pills store is definitely based on a Rite Aid pharmacy store, but which one?
R* have probably made their own generic version of these buildings, but used a few elements from the real life stores, so I don't believe we will ever find the exact match for You Tool or the strip malls.