Question: Recently I had new granite counters installed with an under mount sink. My question is should there be a gap between the sink and the granite? I was told there had to be a shim so it created about a quarter inch gap that they heavily siliconed, but this doesn't seem right.
Answer: Your instinct is right. I couldn't think of any reason to have a shim, nor could I find any evidence to support this by consulting Moen and American Standard installation instructions.
The sink should rest flat against the granite. The wider the gap, the more chance you have of problems later on.
It is hard to speculate on why they might have put in a shim. And to be honest, there could be some good reason. Maybe there was some irregularity with the bottom of the granite counter? That doesn't seem plausible, but it's all I can think of.
If the shim is made of wood, then you really are in trouble and absolutely should have it replaced. Moisture infiltration will quickly lead to rot. If the shim is made of a material that does not rot (scrap pieces of granite or something like that), then you are in better shape.
The first step might be to ask the installer why he did this, and find out if he had a legitimate reason for doing it. Remember that, by doing this kind of work, he has voided your sink's warranty.
As an example, American Standard's undermount sink warranty states: "This warranty shall be void if the product...was not installed in accordance with American Standard's instructions."