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I'm assuming because the X100 has a fixed lens with a leaf shutter. Because of the leaf shutter, maximum shutter speed is limited when shooting at large apertures (for example, it's  to 1/1000th sec. at f/2, 1/2000th sec. at f/4), so an ND filter is needed to enable shooting at large apertures in bright light such as daylight, otherwise it would be overexposed.

X-Pro1 and X-E1 have interchangeable lenses and do not have a leaf shutter. They can both shoot up to 1/4000th sec. wide open, and so don't strictly have a need for an ND filter. Also the fact that the X100 has a fixed, built-in lens may make it easier mechanically to implement a built-in ND.

I love having a built in ND available, so I would like to see it done in the X-Pro1/X-E1 line, but it might be not possible or impractical. Also, if you want to use the ND to blur water, 3 stops really doesn't do enough, for that you really want 6+ stops of ND anyway.