It's not so puzzling when you consider that the 052D is the all-around best destroyer for its tonnage, which is still significant smaller than the 055's. In other words, you don't need a 10,000-ton large destroyer for everything. In many cases, a 7,500-ton multirole destroyer will suffice, and its lower operating costs and upgradeability is also likely a major attraction for its continued usage.
It would seem that the PLAN is pursuing a fleet structure not unlike the USN's - the 055 is akin to the Ticonderogas as the 052Ds to the Spruances (or the Burkes, if you prefer). The key difference is that these Chinese destroyers are significantly more capable than their American contemporaries. That being said, I wouldn't be surprised if the PLAN eventually settles on a 052D/E:055/A ratio of around 2:1.
It's only sensible, and more flexible, to employ a healthy mix of more medium-value, medium-capability ships and fewer high-value, high-capability ships, than to focus production purely on the latter.