Without butting in too much, can I just ask what wattage your soldering iron will be, as you've stated that you've never done SMD rework I'm assuming you've mostly done through-hole soldering in the past, what pitch have you soldered to before? Replacing any connector isn't impossible but as a USB port has 4-5 pins depending on the choice, you've got two pins for the current connector and I'm not entirely sure on the size difference between a 3DS port and a USB port but I'm assuming you'd also lose a lot of the structural support from the grounding pins, which could mean a loose connector which could be prone to breaking, which would be very difficult to repair. I'm not saying it's impossible but I wouldn't recommend you attempting to replace a charging port if you've never tackled SMD soldering before, the basics are simple enough but when you've got SMD and through hold on one port due to the ground pins on the body of the port, if you don't know what you're doing you're very likely to make a mistake and kill a pad if using an iron or improper use of a rework machine.
From what I can see the ground and power pin match so if you removed the data pins from the USB port you'd not have any issues with shorting or reversing the connection but I'm quite sure the pins wouldn't be aligned on the pads so you'd have to take extra care there and again, the lack of proper support for the connector is likely to cause many issues in itself. It might be a cool idea but it's not the smartest sadly with too many variables for someone inexperienced to attempt. I'm much more a fan of replacing like for like and using a modified cable if it makes you happy.