As I understand it, beans were included as kitniyot because they grew in the ground next to wheat.
However, if you grew the beans hydroponically, would they still be classified as kitniyot?
Yes. The real question is do you say "ha'adamah or "she'hakol" on them.
The issue is that it is still by definition a bean. Per the OU: The Mishnah Berurah (453:6 & 464:5) cites three reasons for the minhag (a) kitnios is harvested and processed in the same manner as chametz, (b) it is ground into flour and baked just like chametz [so people may mistakenly believe that if they can eat kitnios, they can also eat chametz], (c) it may have chametz grains mixed into it [so people who eat kitnios may inadvertently be eating chametz]. The fact that it is grown hydroponically changes nothing about the potential processing of the beans.