It's hard to say what the limit of the program is, but its usually storing those URL's in memory so the bigger the list and longer it has to run removing dups, your memory is going to increase and things could slow down.
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Just to share our experience, it can handle MASSIVE lists. We've run through files as big as 1-2GBS before - Though it DID take a few hours to work through it.
As S4ntos said, the real limit is memory - if you have enough ram it will work, otherwise chunk the list up and do it in parts.
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As S4ntos said, the real limit is memory - if you have enough ram it will work, otherwise chunk the list up and do it in parts.