Screw pockets are a great way to put projects together, but are unsightly. If the pocket holes on your project are going to show when it’s done, there’s a great (and easy) way to hide them. All it takes is glue, dowels and some hand tools. You can even turn pocket holes into a decorative accent.
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Nope. In my opinion, it’s not worth the bother. Mortise and tenon joints are usually stronger, or tongue and groove, or even dovetail joints. If the pocket hole joint should start to fail, you can’t re-tighten the screws if their holes are filled! Somewhat matching dowels will be hard to find, could be made on a lathe (it’s more difficult to do that than it looks) but a perfect fit will be hard to achieve. You risk tearing out the pocket holes and thereby weakening the joint, which isn’t all that strong to start with. When sanding the the filled holes flush, or when just trying to, you will tend to create a depression at the intersection of the 2 connected pieces unless you sand the entire assembly uniformly down (say, with a drum sander). Pocket holes can (potentially) make alignment easier and faster, especially if you don’t have a biscuit saw or router table. But if the holes create significant cosmetic issues, it’s best not to use them.