In my experience, using custom decks generally has a positive impact on your spectators, provided that you're not performing a ton of gaff magic. If you're just using the cards for your solid sleight of hand routines and are openly and freely allowing the spectators to examine the deck between effects, they won't ever assume anything is wrong.
For me, the logic goes like this: If you pull out a strange locked box with tubes and crap sticking out of it and then make a dove appear out of it, they might assume that there was something gimmicked about the box. The cards play differently, however, because your audience knows what cards are. They've seen different kinds of playing cards before and they immediately file your new deck into that same category in their mind. They don't do magic, so other than marking cards, they're not really going to have much of an idea as to how you could possibly gimmick a deck of cards.
So far, that only suggests the lack of a major downside to using custom cards, but I made the statement earlier that custom decks can have a positive impact on your performance. Here is how I think that works.
When you open your set and first pull out your custom deck, acknowledge the fact that you are using a custom deck. Say something like, "check these out - they're the new Bicycle Guardians," and then hand the deck out. This accomplishes a few things.
1) It allows your spectators to examine the deck for a reason other than to check and make sure they are normal. (By saying, "make sure these are normal," you are implying that they could theoretically be gimmicked. This is bad. Obviously.) But, in the end, they still get the same psychological effect. They held the cards freely. You couldn't let them do that comfortably if you knew they were gimmicked in some way.
2) It points out that the cards are made by Bicycle (assuming you're using Guardians and not Jerry's Nuggets or something) which only suggests further that the deck is normal.
3) Speaking about the cards as if you value them subtly suggests that you are good at what you do because you use a deck of cards that is of higher quality than they usually would for their beer / poker nights. Professionals use professional equipment. If you're a recording engineer, for example, you use Pro Tools or something similar. Consumers use things like Garage Band. That same logic will apply in their mind, so you will get just a little bit of credit for being good before you even begin performing and that little bit of credit will likely influence their future perceptions of the effects you perform.
Dana