The front wheel is where aerodynamics really plays a part as it's on the leading edge of the bicycle. The tradeoff being that you don't have a lot of weight over the front wheel to control something super deep when it's windy.

However, if you are in the aerobars, your elbows are going to be more over the front wheel and therefore you will have more weight towards the front end of your bike. This is why it's a lot easier to control a deeper wheel on a time trial bike. If you are doing a lot of sub 30K time trials I would absolutely go with a deeper front wheel, you may even want to consider a 58mm up front versus the 50.