<p>A Bowden tube extruder (like the stock one on an Ender 3) is known to have issues with printing the most flexible TPU, and with filaments that (either due to composition or condition) don't take well to too much retraction -- though the latter can be ameliorated somewhat with slicer settings.  Direct drive extruders, on the other hand, by reducing the extruder to hot end distance to the practical minimum, greatly reduce the amount of retraction needed as well as the effect of filament compression and stretching.</p>
<p>One potential down side I'm aware of is that putting the extruder stepper and drive on the X carriage adds mass that the X drive motor has to both accelerate and decelerate; this could in theory have an effect on print quality, increasing ringing and overrun on the X axis (though this isn't generally a problem with the steppers used on the Ender 3 and similar printers).</p>
<p>What other reasons might there be to prefer a Bowden tube over direct drive?</p>

Other than higher carriage mass as you already noted, the only other reason to not go with Direct Drive over Bowden is the higher level of maintenance required. In most cases Direct Drive will provide advantages such as increasing the maximum flow speed, enabling the use of Linear/Pressure Advance, shortening Retraction moves, and better resistance to obstructions in the filament path, and more reliable printing of flexibles as you have already noted. As well, A direct drive system would allow a less-powerful stepper motor to be used, which cuts down on the carriage mass problem.