You're right, seams play a bigger role when you're texturing in 2D instead of 3D. However, it's still good practice to careful where you place the seams, especially if there is a difference in resolution. (Changes in resolution are especially noticeable with bump maps and displacement maps. I learned that the hard way.)
That being said, it does make sense to split the body up into parts when you're UV mapping. For instance, usually the head maps need a larger part of the UV space so the details will have enough resolution to look crisp.
Short answer: It's okay to split your model up into parts, but even if you paint in 3D, still be mindful of where you put the seams. Hopefully that makes sense. Good luck with your model!