Extract value from JSON ARRAY in BigQuery

Consider below approach with more explicit alignment of respective entries

select json, 
  array(
    select 
      if(
        json_extract_scalar(val, '$.apples') = '5',
        struct(
          json_extract_scalar(val, '$.oranges') as oranges,
          json_extract_scalar(val, '$.pear') as pear
        ),
        struct(null, null)
      )
    from t.arr val
  ) fruits
from `project.dataset.table`, 
unnest([struct(json_extract_array(json, '$.fruit') as arr)]) t      

It is less verbose and has output of fruits as a repeated record as opposed to two arrays
If applied to sample data in your question output is

In case if you really need to keep output is separate columns - use below

select json, 
  array(
    select 
      if(
        json_extract_scalar(val, '$.apples') = '5',
        ifnull(json_extract_scalar(val, '$.oranges'), '0'),
        '0'
      )
    from t.arr val
  ) as oranges,
  array(
    select 
      if(
        json_extract_scalar(val, '$.apples') = '5',
        ifnull(json_extract_scalar(val, '$.pear'), '0'),
        '0'
      )
    from t.arr val
  ) as pear
from `project.dataset.table`, 
unnest([struct(json_extract_array(json, '$.fruit') as arr)]) t       

with output

When working with array_agg

an error is raised if an array in the final query result contains a NULL element.

You can try using a string 'null' like this:

with `project.dataset.table` as (
  select '{"fruit":[{"apples":"5","oranges":"10","pear":"20"},{"apples":"5","oranges":"4"},{"apples":"5","oranges":"9","pear":"40"}]}' as json union all
  select '{"fruit":[{"lettuce":"7","kale": "8"}]}' 
)
select 
  json,
  if( regexp_contains(json, '"apples":"5"'),
    (SELECT ARRAY_AGG(ifnull(json_extract_scalar(arr, '$.oranges'), 'null')) from UNNEST(json_extract_ARRAY(json, '$.fruit')) as arr ),
    ['null']
  ) as oranges,
  if( regexp_contains(json, '"apples":"5"'),
    (SELECT ARRAY_AGG(ifnull(json_extract_scalar(arr, '$.pear'), 'null')) from UNNEST(json_extract_ARRAY(json, '$.fruit')) as arr ),
    ['null']
  ) as pear,
from `project.dataset.table`