$_internalConstructNdvSketch is implemented only as a classic accumulator. As a result, any $group containing it is ineligible for SBE pushdown and executes in the classic engine. 

A lot of future QE performance work (e.g. scan performance) will focus on SBE. Providing an SBE implementation (presumably wiring up the exact same hyperloglog implementation to SBE hash agg / the VM) seems like a good piece of future work.