I would say I am an NYC Coffee Shop veteran. I have lived here most of my life and been to tons of coffee shops. The majority of which have come and gone with little fanfare and had music systems with the brand name of Sony, Peavy or Bose. The New York crowd rarely goes to a coffee shop to spend more than 10 minutes. Those that do go to do work, etc. These people often have iPods or other devices to drown out the background (NYC is a noisy place after all). They may appreciate good sound, but need isolation. Then, there are the people that go to a place to talk with other friends or on a date. Not really paying attention to the music quality as they should be listening to the people they are with. The rare exception are those that just go to hangout. These are the ones that may notice the sound on a more regular basis. That is the person that is really the only person that hears the sound and may notice it in detail. I, personally, only notice when the sound is awful in a run of the mill coffee shop/restaurant.
There are exceptions. However, it is not usually the sound of the house system that I notice. Let me explain. My favorite coffee shop in the city was DTUT. It was laid back and rustic and had eh sound as I don't remember it one way or another really. I remember the music, but mostly because the people who worked there played the music they liked (and the choices were, to say the least, odd). However, open mic night occurred on Wednesday night. Music from 6-11pm. All live, all bring your own instruments. The musicians got 2-3 songs each. Most of them were from the Anti-Folk movement as the person running the show was Amy Hills (who had minor success in the movement, but never got farther. I did catch Regina Spektor about 50 times in similar situations, though never at DTUT). That was when the sound was important to the place. But, well, the sound was provided by the musicians and the "stage" system, not the house system.
One other point. Margin wise, I am not sure speakers is where a new coffee shop should spend its money. There is a lot of competition out there in NYC. Most people are not coming to a coffee shop for sound. I would spend the money on what brings people to the place, including a good "stage" setup if there will be an open mic, good coffee, etc. and not worry too much about the main sound (so long as it is serviceable).
Shawn