I design a lot of PCBs that uses microcontrollers with external clocks. For some reason a lot of the example designs always tend to use the big generic HC-49 package. Even factory made modules that I purchase tend to use that package. I typically source my components from LCSC which has a large variety of components. Are there any disadvantages to using the smaller packages for crystals other than price and availability?
Crystals have much more important properties than frequency, size and cost. These are operating temperature, frequency and temperature tolerance, load and shunt capacitances and ageing.
Obvious advantages of HC-49's size - easiness to mount and power dissipation.
But I did not see industrial or enterprise designs using HC-49 last decade (even on big boards where HC-49 will fit). The biggest they use is HC-49S, or chip crystals.
Certain packages can offer different sets of frequencies. For example, the 3.2x2.5 package can be had with frequencies up to 80MHz, and with tolerances of 10ppm.
Parasitic capacitance and inductance also comes into play, the 2 vias of the HC-49 and the 2 large pads of the HC-49S have larger parasitic capacitance than the pads of a small SMT device.