Does shape affect pasteurization time when cooking sous vide?

It depends on what is to be pasteurized. If one aims for pasteurizing the surface only, then the shape is more or less unimportant. If however one wants to pasteurize the core, then the shape will affect the times.

To be on the safe size, measure the thickness where the meat is thickest.

Myhrwold writes in http://forums.egullet.org/index.php?/topic/116617-sous-vide-recipes-techniques-equipment-2004-2010/page_st_120_p_982720#entry982720 about cooking times (not pasteurization times):

This is true for any kind of cooking actually. Most of what we are taught about cooking is actually wrong. For example, anytime somebody tells you it is “10 minutes per pound” they are saying something that cannot possibly be accurate, because this would imply that cooking time is proportional to the weight. If you take something like a whole bird and scale it up you will find that cooking time is actually proportional to something like (weight)^(2/3) – weight to the 2/3 power. This is because increasing the weight scales up the thickness by the cube root. Since most people are not accustomed to taking things to fractional powers, people substitute a linear relationship. That might work out OK in practice over a small range, but it can’t be accurate over a large range. For example, if you double the weight, the linear relationship would tell you that you double the cooking time. The 2/3 power would tell you to increase it by 59% - that is a pretty big difference.

As a general rule of thumb heat diffusion times go as the square of the thickness increase. So, doubling the thickness results in FOUR TIMES the cooking time. That is a rough general rule of thumb, which is not perfect but it illustrates the nonlinearity of the system. I don’t know why this isn’t taught to chefs more often because it is a fairly easy thing to grasp and use.

A side note:

If you have an iPad or iPhone then I can recommend SousVideDash. One must enter meat type, shape and size, initial and final temparature. Then graphs are drawn that shows pasteurization times for both surface and core (or more precisely graphs of the reduction of salmonella and listeria).

See the website:

http://www.sousvidedash.com/

I hate answering food health questions, but for non-ground meats, I have heard that all of the risk of bacterial infection is occurs on the surface of the meat, making shape irrelevant. This is because the infection risk comes not from the handling of the meat, not the meat itself. (There's an exception for Kreuzfeld-Jacob disease, which you can get from non-ground roasts served on the bone, since that's where the prions concentrate.) For sous-viding ground meats (sous-vide and blowtorched burgers, yum!), you should be careful to cook for the full time, as ground meats can have bacterial issues (e. coli especially) all the way through.