You're absolutely correct: "I need" is logically sound. However, "I'll need" sounds more polite.
Although the other answers posted here state that "I'll need" is more correct because the clerk really needs the credit card information in a few seconds (presumably when he enters in the number), technically it sounds like he needs the card right there and then, so I don't believe that's quite the right answer.
So why does "I'll need" sound more polite? Saying "I need your credit card" sounds like a demand, akin to "Give me your credit card." Throwing in extra words, like conditionals ("Would you pass me the salt?" vs. "Pass me the salt"), tends to sound more polite, even if the sentence without them is technically correct. It somehow softens the blow of something sensitive like asking for someone's money.
EDIT: I realized that this doesn't address the other question: why it's "I'll have to get back to you on that" vs. "I have to get back to you on that." Again, I agree that the latter is technically correct. Right now, I have to get back to you on something, even if I end up getting back to you at some point in the future, like saying "I have to get some milk." The thing is, that particular phrase is an idiom, and there's really no explaining idioms. It's just how it developed and how we're used to hearing it, and you better say it that way or it'll sound off to everyone.