One of the major rules of illusion, especially card illusions is to not make unneeded moves due to the fact that it raises questions in the viewers mind. Using something like a standard bicycle deck helps to remove that thought of something "fishy". Having a custom deck brings the thought of "if it looks weird, it probably is weird".
Like all magicians, I've made mistakes performing, but I try to work it into my routine, and I've had more questions over custom decks than bicycles. Maybe that is just my experience, but I'm sure others have had the same.
Additionally, I try not to use decks that tout super smooth handling, etc... I'd love to have some of the brown beauties for my collection of decks, but I wouldn't perform or practice with them. I tend to use other peoples decks as much as I can, doing a trick with a deck that they own is much more interesting to them as they know it's not rigged. Much better when you load your gaff into their deck.