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Operation speed
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As phrased and assuming no indexes, and depending on the version of SQLite3 in use, then yes.  Since you did not mention whether or not there are any indexes or the version of SQLite3 that would be an exercize called "20 Questions".

Create an index if there is not one on values_11 if not already one where the first column is uint64_pointIDX on that column and change the delete to:

```
delete from points_11 
      where not exists (
                        select * 
                          from values_11 
                         where points_11.uint64_id == values_11.uint64_pointIDX
                       );
```

so the number of operations is limited to be proportional to the number of rows in points_11 and a table scan of values_11 is not required.