I think we can say pretty safely that they track multiple decimal places. How many decimal places that might be is of course, hard to answer; but the argument I'd make is this:
If it were rounding off to the nearest percent, it would be impossible to have a miss rate between 0 and 1%; that is, if you could miss at all, you'd miss, on average, one in every 100 attacks. However, rogues have taken data sets with miss rates demonstrably below this - the first one I found searching around is
this post wherein a rogue attacks 10286 times and only misses 5, which is statistically significantly different from 1% miss rate and clearly not 0% miss rate. So it's certainly not rounding to the whole percent.