I know I'll get attacked for this, but I really like The Wreck of the Richard & Charlene in Mt. Pleasant. It really fits the definition of hole in the wall, being at the non-touristy end of Shem Creek sandwiched in between Wando Seafood Co. and Magwood Seafood (pretty much the only two local shrimpers left). It has no A/C, but in October it should be perfect. You walk through the kitchen and into a back dining room/screen porch area overlooking the shrimping boats and marshes. I love the full seafood platter, which includes shrimp, oysters, scallops, and fish, with red rice, red cabbage, and a hominy square. I live in Charlotte, NC, and I find it worth the drive just to have some fresh-off-the-boat seafood and salt air. Yes, it's more expensive than other fried seafood platters you'll find in the area, but they are committed to a local product (sourced from Wando Seafood Co.) and that comes at a cost.
Also in Mt. Pleasant as you head towards Sullivan's Island is Buddy Roe's Shrimp Shack. They refuse to serve anything but local shrimp.
For non-tourist try The Marina Variety Store Restaurant at the municipal marina.Its old fashioned and frayed around the edges,but its good,fairly priced and you won't see a single fanny packed yankee cruise boater.
For hole-in -the-wall and close to Folly, try Bowen's Island.The local oysters are great and everybody has to go there at least once.Folly beach proper is lacking in good seafood unless something new has happened recently.
Another good downtown choice is Pearlz Oyster on East Bay.Its really a bar that happens to have great simple seafood,go early to avoid the roudy bar scene.
Marina Variety Store and Restaurant
17 Lockwood Dr Ste E, Charleston, SC 29401
Pearlz Oyster Bar
153 E Bay St, Charleston, SC 29401