Phase issues are HUGE with subwoofers and dominate performance characteristics. Yes, a port is out of phase at some frequencies, but coherent at others, hence the concept of tuning. The increased output is due to coherent coupling of the front and back waves.
Bass can be considered omni-directional when the enclosure is placed in a space. You get loading or directionality effects from adjacent surfaces. You also get reflections. Reflections are the killer and why boxes in trunks perform poorly of not baffled. Simple math can determine the reflected path lengths and resulting phase interference. If a sub is placed 4 feet from a reflecting surface, the additional path length is 8 feet, meaning cancellation for a 16 foot wavelength.
With multiple subs, the cones are usually side-by-side, creating a line array. This is usually ok. Where people run into issues is with complex configurations with larger distance differences. Again, it is all about path lengths.
Another thing to consider is that below a certain frequency, we are simply pressurizing the cabin since the wave never fully develops.
And when comparing one vs two subs, excursion comes into play. Two subs don't have to work as hard to have the same output as one, assuming coherent sources. This reduced excursion allows the voice coil to operate in the magnetic gap, increasing accuracy. But with one nice sub you can get an underhung model which eliminnates this benefit.
So much to consider, a lot is personal preference.
I run two because they are trunk baffle mounted and coherent. I also have fairly low power and efficient subs, and given their age I want to operate them at lower excursion. I could get one nice sub to outperform these.