Is it true that aquaponics yield crops with a lower nutritional value than soil-agriculture?
First look at the article, is cites no sources and is not written by an an expert. It is written without peer review and does not seem to understand how to measure nutritional content (brix is only a measure of sugar not minerals) or what controlled conditions are. No methodology for collection, type of hydroponics, sample size, or anything else is given, this is important becasue many many thing unrelated to the farming method can effect Brix. So you can safely ignore the unscientific claim of the article and go with scientific ones, which show no difference when tested. 

First always look at the source of a claim and when in doubt search google scholar first. 

This is clearly editorial click bait.