The Rapid Fire upgrade increases attack speed for the Monkey Ace, allowing them to deploy weapons more often. Although the timing at which the Ace may deploy weapons may seem like it is disrupted, strictly speaking an attack speed increase is actually overall better for the Monkey Ace, because adding more attack speed will increase the consistency of its attacks too. Therefore, more weapons can be deployed per second, increasing damage potential of the Monkey Ace.
Rapid Fire's base attack speed bonus has been reduced, but overall attack speed with this upgrade is exactly the same. Therefore, it was not nerfed overall, but rather buffed overall because of another buff inherited into the base Monkey Ace.
Rapid Fire attack rate buff decreased (0.6x → 0.75x). Base attack speed remains the same.
Despite being the 3rd upgrade in BTD4, it became the first upgrade in each path in BTD5 and BTD6.
Prior to Version 23.0, there was a special case for Spectre and Flying Fortress that increased their attack speeds by only +33% instead of +66% for all other upgrades. This has since changed to a plain +33% for all since then.