Comparison of 1d and 3d accelerometers
This is an absolute no-brainer, even if just because if you use three 1D accelerometers, you will never be able to align them to the precision to which a 3D unit is aligned off the shelf.

At best, accuracy of measurement will be a toss-up.  If you use analog accelerometers, writing code will also be a toss-up, but if you use  digital unit/s with some sort of serial bus, digital wins coding ease hands down.  For all the other criteria, digital comes out on top as well.

If I'm missing any factors, they probably have to do with the specifics of your project, which you haven't shared