I work in the water quality field and have taken a few thousand secchi readings. More important than size of your disk is consistency in how you take your reading. Always take it in the shade of the boat and never with sunglasses on. Ropes are also a bad thing if you are taking depths deeper than about 3-4 feet; most ropes stretch when wet and will give innacurate data. The disk should also be painted in non-reflective (flat) paint.
The only reason you should worry about the size of your disk is if you want to compare numbers with other people or reference info. A small disk will disappear slightly sooner and a larger than standard disk will stay visible for slightly longer.
Using a standard size disk is also helpful when you lose the first one and can't remember its dimesions. I've had two coworkers lose disks when they just simply dropped them.
