Horizontal pieces of wood that form wainscot framing are called rails and vertical pieces are stiles. And while it’s true that the joinery connecting stiles and rails doesn’t have to be strong, ordinary butt joints won’t cut it either. Seasonal wood movement will open the joints, making you look bad. Pocket screws are an excellent option for joining stiles and rails into frames before these parts get fastened to walls.
If you want to raise your game a notch, consider interlocking profiles for stile and rail wainscot joinery. One unique option uses a symmetrical bit in a table-mounted router made especially for this job. Use it to mill a positive profile along all inside edges of the stiles (mill the stiles outside face down), then flip the rails over (inside face down) and use the same bit (with the same height setting) to mill a matching profile on the ends of rails. This creates a decorative profile that allows enough joint contact area so stiles and rails can be glued together securely as they go on the wall, one piece at a time. You’ll find it easier and safer to mill the end grain of wide pieces of wood for the rails, and then saw them to width after routing.
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