The biggest downside is their frailty. When it comes to tenon and mortise joints, the tenon's face grain cheeks are totally in touch with the mortise's face grain side. In this case, the adhesive also works effectively. But with dowels, there is a gap between the two pieces of wood because they come from different directions. So when dry, they have nothing to hold them together.
Also, be careful not to split your dowels during use if you are using them as a handle. They need to be of a sufficient diameter so that they do not break under their own weight.
Dowels are also very expensive compared to other types of hand-made joints. A full set of 10 standard size dowels can cost up to $150. But they are worth it because they last forever and require no glue or paint.
Finally, dowels are difficult to join with outliners because they don't fit properly. For example, it isn't possible to use them as a substitute for handles because the ends aren't round like a ball would be. Instead, they have flat faces that don't match up with most outliner plates.
People often think that only large items can use dowels as joints because they believe that it is impossible to get a perfect fit with such small pieces of wood. This is not true!
The downside of mortise and tenon is the poor quality of construction. The wood can shear on any side if the proportions are off. As a result, mortise and tenon joints are extremely difficult for the do-it-yourselfer to manufacture. They require a jig or vise to hold the pieces together while you cut each one individually.
Mortise and tenon joints are also only suitable for flat surfaces. If you want to attach two edges that aren't parallel, such as the corner of a sheet of plywood, then this joint isn't for you.
Finally, mortise and tenon joints are very inefficient at transferring load from one board to another. Because so much material is removed in order to create the hole, there is a large area of weak wood that doesn't contribute to the strength of the joint. Even if you use fairly thick boards, they will still be quite thin where the tenons connect to them. This is why most mortise and tenon joints are used for decorative purposes only; they serve to give the appearance of a strong joint when actually there is a very weak connection.
There are several ways to improve upon the traditional mortise and tenon joint. A dowel pin joined with a wooden peg provides more uniform strength across the board face and increases resistance to twisting forces.
Pocket holes were just half as robust as mortise and tenon joints. However, a joint that is half as strong as a mortise and tenon joint is actually very enough for a quick and filthy project. The dowel joints outperformed the pocket hole joints by 1.5 times. Dowels are much more stable than pocket holes because they don't have any physical contact on their own surface which allows them to span greater distances.
Also note that while pocket holes require drilling before you can use them, dowels can be used immediately after they're cut.
The lesson here is that if you need something sturdy but can't be bothered with precision or appearance, then go for it with some dowels and some glue!