Growth is important because it is what separates a start-up from other companies http://www.paulgraham.com/growth.html

But YC knows very well that there can be many reasons for slow growth. Many times easy to make changes can have big effects on product/market fit and growth rate. And YC is great at helping with that. So don't be afraid to apply even with flattening growth, it is called an accelerator for a reason.