It's mostly about signal-to-noise. The drawback to those detectors is that because the nuclei are heavy, when the neutrino interacts with them, they don't end up moving very fast and so there isn't much of a signal produced in the detector. They have to be cooled to cryogenic temperatures to even have a chance of seeing a coherent scattering event above thermal noise. Yes, the interaction cross section for the neutrinos is larger, but you can't pick out individual events very easily.

The 2017 paper you linked is the first observation of the process. They had to do it statistically; there's no smoking gun event. It took them almost a year with the thing sitting next to a neutron beam to get enough statistics. With a beam, they were able to do extra noise rejection based on the beam timing. It's still a lot of experimentation and engineering work to go from that to something that can operate in a lower signal-to-noise environment.

Also, growing large scintillator crystals is a very specialized process and so they are expensive. The cost is going to limit how large you can make such a detector. You can scale up a water-based detector much more easily, and that extra mass can make up for the reduced cross section, depending on what you are trying to observe.