The performance numbers you cite are not from this article and are unrelated to this work.
Homomorphic encryption has seen massive performance improvements over the past years. A single multiplication of such small numbers with SEAL would take around a millisecond. In an amortized setting the time would be closer to microsecond.
Search from O(billion) item data sets can be done with an encrypted query in seconds when done right. A complex SELECT-statement might be hard as SEAL at least is based on arithmetic circuits, whereas such queries may have much more convenient Boolean circuit representation.
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