Using Sourdough Breads to reduce Fructans
There isn't really any scientific information available about the fermentation of fructans in sourdough. I did find this page which says that there are some lactobacilli that are effective at breaking down fructans, but the effectiveness varies by strain of bacteria and type of fructans. (There are also many lactobacilli that don't break down fructans: of 712, only 16 were effective.)

While a longer fermentation time will mean more of the sugars in your dough are digested, since you are aiming to ferment a specific type of sugar, the establishment of your starter may be more important. According to this study, a couple of the strains of lactobacilli shown to be effective at breaking down fructans are found in well-established starters. 

In short, rather than giving your dough a long fermentation time, it may be more effective to make dough with a high proportion of a well-established starter instead. The starter will have had a longer cumulative fermentation period to break down fructans, and if your starter has the appropriate culture, it will be more effective at breaking down the fructans in the added flour of your final dough. There is little research on this specifically, so this is largely conjecture and entirely dependent on the culture of your starter.