Aquifers are extremely intimidating for newer players who haven't screwed around with any pumps or anything like that, and such players are fairly likely to embark on at least one aquifer territory during their newbie stage. They have no idea how to even begin approaching the obstacle, so they utterly fail to make any progress at overcoming it at all. They abandon and embark where they have no aquifer. Even as they become more experienced, they still remember aquifers as something that was completely impenetrable, both in concept and in practice, and they communicate that attitude to other newbies.
In addition, until relatively recently, the best aquifer-piercing methods known were complicated, difficult, dangerous, and resource-intensive. Particularly for multilayer aquifers, getting through them was quite impractical, would take months of dwarf-work and hours of player-time, so even the more experienced players who otherwise knew how to pierce aquifers avoided it because it wasn't worth the effort. With the development of the double-slit piercing method, the whole aquifer situation changed radically, as it is a simple, cheap, safe way of defeating them, but that was only discovered a bit over a year ago and, due to people avoiding aquifers in general, hasn't been disseminated as widely as several engineering developments in other fields have been.