Performance analysis indicates that SQLite spends very little time doing bytecode decoding and dispatch. Most CPU cycles are consumed in walking B-Trees, doing value comparisons, and decoding records - all of which happens in compiled C code. Bytecode dispatch is using less than 3% of the total CPU time, according to my measurements.
So at least in the case of SQLite, compiling all the way down to machine code might provide a performance boost 3% or less. That's not very much, considering the size, complexity, and portability costs involved.
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