If you can use duplex breakers, is there ever a reason not to?
Double-stuffing has its limits

In addition to any limits that your loadcenter places on the use of double-stuff breakers, there are also limitations on the breakers themselves due to the smaller effective frame sizes involved.  As you have noticed, one of those limits is that double-stuff is incompatible with AF or GF functionality, or with other special functions/ratings such as the HID rating used in some commercial work for breakers that are used to switch heavy lighting loads on a frequent basis, or the Switching Neutral function used for fuel pumps and some generator transfer situations for that matter.

There are other restrictions in play here, though, and chief among them is that the smaller frame size sets an ampacity limit on double-stuff breakers.  While a 1" or 3/4" frame can normally handle 125A/pole, double-stuff frames are limited to 50A/pole for 1" breakers (HOM, QP, BR, THQL) and 30A/pole for 3/4" breakers (CH, QO).  Furthermore, double-stuff breakers are also limited in terms of their ability to interrupt large amounts of short-circuit current.  This isn't an issue in most light-duty situations, but their 10kA fault current limit becomes a consideration in multi-family and commercial work where larger services are found.

Finally, double-stuff breakers are limited in their ability to accept breaker accessories; for instance, they can't be used with generator interlock kits and require special lockoff devices.  This also extends to electrical accessories, as these breakers are not available with features such as shunt trips that can kill the power remotely or auxiliary/alarm switches for indicating the status of the breaker to some automation system, either.