A 100 mL beaker does not hold exactly 100 mL. To be perfectly honest about it I've never poured 100 mL (say from a graduated cylinder) into a beaker for the purpose of seeing how much the beaker will hold; however, I suspect they will hold slightly more than 100 plus or minus 4 or 5 mL. Most beakers are marked these days (some at 25, 50, 75 mL) but the marking are not exact. They are useful for approximate dilutins but not for quantitative work.
No, the rated capacity of a beaker does not mean that it has to be filled to the brim. The rated capacity refers to the maximum volume that the beaker can hold, which in this case is 100ml. You can choose to fill the beaker with any volume of liquid up to its rated capacity. You can fill it partially or fully depending on your needs or the specific measurements you require.
