There is little difference between the two with regard to running homebrew. The only possible difference would be if you wanted to use a slot-2 device with a very old PassMe-style device, which would only work on DS Phats with firmware 3 or below. In all likelihood however, you'll be getting a slot-1 device, and even if you get a slot-2 device you'd get a NoPass instead, so you don't need to worry, as those work on all DS systems.
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