I think that "Can you hurry it up?" is used if you want to be impatient or sound somewhat rude. In comparison to "Can you hurry up?" But they do mean the exact same thing.

Same meaning exactly. "It" seems more precise, but if we as someone to hurry up, it always refers, either implied or explicit, to some task - getting ready, repairing something, etc.

The difference is very small, and in most cases they mean the same thing, but the emphasis is slightly different. "Can you hurry it up?" means the task (it) or "you" is the cause of the slowness. "Can you hurry up?" means "you" is the cause of the slowness. I would say "Can you hurry up?" if I felt that the person were going too slowly. For example, we are walking together, and they fall behind me. Maybe I felt they were being lazy. When I say this, I blame the person for the slowness. I would say "Can you hurry IT up?" if I were waiting on a person to finish working on a very slow computer. It would not make as much sense to say, "Can you hurry up?" if the computer (it) is going slowly, not the person.