You are probably thinking of dowels used as loose tenons, where a blind hole is drilled into the mating pieces of wood and the dowel is not visible once the joint is together.

Sometimes people glue a butt or mitre joint, then once the glue has set, drill a through hole for a through dowel from an outside face of the joint.

The blind holes approach is tricky to get perfect alignment on where dowels are being added across a longer length. As a hobbyist I've tried a few cheaper dowelling jigs and had mixed success. This challenge lead to other loose tenon solutions like biscuits or dominos which allow for some side to side misalignment while retaining the ability to keep the visible faces aligned.

The through dowel approach avoids the misalignment problem, but comes with the visibility of the end grain of the dowel on one exposed face. Some people are ok with that.

Dowels are still one of the "strongest" options for end-grain to long-grain joints. Many professional woodworkers now favour dominos simply due to who quick it allows them to work and the additional allowance for some side-to-side alignment.

Easiest way is to drill through, then cut and sand the dowel flush; leaves a round circle where the grain doesn't match for each dowel.