Part cooling is essential to print at any decent vertical speed (layers per second), which is critical if you do rapid prototyping of small parts or vase mode prints. This is because you can't (repeatedly) print on top of material that hasn't yet cooled enough to be rigid; if you do, after a few layers, you'll find nothing is in the right place and it's all a bunch of goo getting dragged around by the nozzle. In fact, if the part is small enough you might not be able to print it at all. That's because, while slicers have features to slow down to guarantee a minimum layer time for cooling purposes, if the hot nozzle sticks around in the vicinity of a tiny part the whole time, just the heat from the nozzle will keep it from properly solidifying.
The Ender 3 (and as far as I know, the v2 as well, along with just about every other Creality printer) has pitiful stock cooling. It's off-center from the nozzle, and aimed more at the nozzle itself rather than the part below it, so that it saps heat out of the hotend (making the heater work harder and reducing your max achievable flow) at the same time it's (barely) cooling the print. So upgrading it is desirable. But, as you've guessed, there are cons too.
Some, especially those utilizing the stock 4010 fan, reduce airflow by constricting the airway too much. The 4010 does not really have the power to compress the air much, so if the airway cross-sectional area decreases along the way, that will reduce flow. Does the increase in focus/delivery to the right place make up for the lost flow? Maybe.
Some focus the air too narrowly while increasing its pressure, delivering high-pressure air to a still molten point on the print. This can actually cause the extruded material to bend in the direction the air is pressing it before it cools enough to solidify, giving an inaccurate print.
Large fans and ducts add mass to the toolhead, which can increase ringing, especially if they're not sufficiently rigid.
Many of the cooling mods mount awkwardly to the toolhead in ways that interfere with the motion of the carriage, reducing total build volume.
If the cooling mod blows on/over the heater block, it can reduce melting performance and pour heat onto the part you're trying to cool. Most try to avoid doing this, but you may find you want additional insulation around the block if you use more powerful part cooling.
Some people will also tell you that "too much cooling" will harm your print quality, hurting layer adhesion, making the print warp, etc. I use a rather extreme cooling system and have not encountered such problems that can't be remedied with a slight increase to the nozzle temperature, yielding better overall quality and equal strength to what I would have gotten with lower fan. But I print just PLA, PETG, and TPU, so it's likely that this could be an issue with other materials like ABS or nylon. If so you can always reduce the fan speed.