The guesstimated annual attendence for Magic Kingdom at WDW, the worlds most visited themepark for 2005, the last year that guesses were made was 16.1 Million guests.
3/4 of that is 12.075 million. Nobody attempts to guess WDW's total attendence. Epcot was 9.1, MGM and AK were both in the mid 8 millions, but much of that is hopper passes. Those pesky multiday passes and hopping ability make it hard to guess.
It's probably safe to just use the MK number though. The number of people that went to WDW and didn't go to MK is probably minescule.
So, yes, the Smithsonian has higher attendance.
That was attendance at Smithsonian venues combined. I expect plenty of people visit the Air&Space museum, the American History museum, and the Natural history museum on one trip. Just like people visit MK, Epcot, AK, MGM on one trip.
In other words, to give a fair comparison, you need to either count unique visitors (i.e. somehow eliminate "hopping" at both WDW and the Smithsonian - as you said, this is tough to figure), or take the combined attendance. By your numbers, the combined attendance gives something like >41 million/year for WDW, vs. maybe 23 million/year at the Smithsonian (and that assumes that the last 3 months had visitation rates the same as the first 9 - not likely since summer is by far the most attended there).
So no, the Smithsonian does not have higher attendance than WDW. If you want to claim that the Smithsonian has greater attendance than just MK, you need to figure out how many unique visitors there were to the Smithsonian. As one example, the Air & Space museum had 9.4 million visitors at its peak in 2003, but was down to 5 million last year**. I don't know that you're going to have any more luck figuring out the unique attendance at other locations. But, it's not clear to me that the Smithsonian unique attendance numbers are going to be higher than MK's.
** See: http://www.usatoday.com/tech/science/space/2007-02-20-space-museum-attendance_x.htm