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.
A key point to keep in mind is that SQLite bytecodes tend to be very high-level (create a B-Tree cursor, position a B-Tree cursor, extract a specific column from a record, etc). You might have had prior experience with bytecode that is lower level (add two numbers, move a value from one memory location to another, jump if the result is non-zero, etc). The ratio of bytecode overhead to actual work done is much higher with low-level bytecode. SQLite also does these kinds of low-level bytecodes, but most of its time is spent inside of high-level bytecodes, where the bytecode overhead is negligible compared to the amount of work being done.