I don't think there's a general answer that fits all applications in regard to this question. Most modern vehicles, at least since multi-port fuel injection became the standard in the late '80's and early '90's, usually have a factory air cleaner that is actually a "cold air intake" by definition. The bigger question is whether the intake system in the vehicle restricts the air flow going into the engine under its operating conditions? If the vehicle and its engine are going to be operating at high RPM for a length of time, then it's possible a less restrictive air cleaner or intake system may be beneficial. As far as the R51 Pathfinders, the stock air box and air cleaner are actually pretty good. On the factory-supercharged Nissan Frontiers and Xterras of the early-mid 2000's, the stock system is pretty small and has several resonators included in its design. I can tell you by personal experience that replacing the factory air intake (which is a cold air intake design) with an aftermarket system like K&N or aFe's does make a noticeable improvement in performance (along with making it a lot noisier, for better or worse). Modern ECM's will be able to compensate for minor bolt-ons to the engine. Older ECM's like used in GM vehicles has its software on a PROM chip which could be removed and replaced easily. Older Nissans had the software on a chip soldered to the circuitboard, so reprogramming consisted of removing and re-soldering a new chip to the board with different software. In the 2000's, Nissan started the move to programmable ECM's (as did most other manufacturers), so performance tuners were developed by companies like Superchips and Diablo which allowed DIYers the ability to reprogram their vehicle's ECM software via the OBD II port using one of several custom tunes on the programming device (i.e. "tow," "91-octane performance tune" or a gas saver tune). These were made for stock vehicles with no or minor bolt-on mods. Those with more serious mods could get an interface to work with their laptop or get the ECM tuned by a professional company specific to their vehicle, i.e. UpRev.
It's all a matter of what you want to do with your vehicle and how much performance you want out of it (or, can get out of it)....which also is relative to how much money you want to spend.