It really doesn't matter, but what is important is having a convention and sticking with it. I like to use strict sass-lint rules to enforce lowercase hex values, and short values where possible (e.g. #fff instead of #ffffff).
Here are my reasons for choosing lowercase;
Easier and faster to type (I have changed the key bindings of my caps key and using shift is just awkward, especially mixing numbers and letters)
It's easier to search for something if you know what to expect. (Say you're rewriting old code to Sass, you've fixed all occurrences of #aa99cc, but what about AA99cc, Aa99CC, A9C, a9c? Linting will pick out these problems for you)
