AFAIK, unless they changed it somehow for some reason in civ4, the 'commerce' equals the net income in gold of your city's worked squares. In civ1 and civ2, the commerce icon were two trade arrows, thus the concept of 'commerce'. Imagine that the gold you see on the squares comes from the taxed 'commerce' taking places there.
One thing I find strange, is no longer to have a tax slider/setting. It felt a bit more right, than just shoveling all the gold produced in the emperor's coffers. Plus it revealed the relation between income and science in a convenient way. I also loved being able to reward the people with more "luxury".
So, to answer the question, banks and markets will function all the way, they're not dependant on how much of your income you spend on science or culture.