I'm a bit confused by the design. Are you saying the shelves have pegboard in them or MIGHT have pegboard in them?
Regardless, leave a gap between the rim of the box and the underside of the shelf. I have helped dozens of people build racks and the number one thing most would go back and change is the gap. Most think the tighter the better, but nothing could be further from the truth.
Trust me, it's easier to fill in too big of a gap than it is to make a gap that is too tight looser.
I shoot for 1/8" or 3/16". With those polycarbonate boxes there is so little flex so they are very secure. Also, I have not found a lot of variation among these boxes in height, which also really helps.
What species is this for? That can make a difference.
My only concern is that I don't understand exactly how you are using the pegboard. It is a flexible material so I want to understand how you plan to use it.
>>Ok I'll be starting to build my rack soon. For the tubs I'll be using 3 12x18x6" and 6 18x26x6" clear polycarbonate tubs that I'm getting from a restraunt supply center. The question is I don't plan on using lids so should I use peg board so that when the tubs are in place the top of the tub is snug against it or should I use a solid piece of wood and leave about a 1/16" between the board and tub. Anyone with experience in rack build your help would be grateful. Thank you.