When I started my selling software, I priced with something.99 too. I did this because everyone else did. I was unfamiliar with these sorts of things so I followed on.
I am sure that in some business at some point, there was a big positive in switching to that sort of pricing.
When I switched my software to whole numbers, I did not notice a drop in sales. Things continued to grow. Of course, my business is one data point and a small one.
How much of why we tend to do this is because, historically or normally, that is how we've seen it done?