I would recommend a different structure to the JSON since an array node can hold both, a value and subnodes. This should be reflected in the JSON. So, for an array:

a(1)="A"
a(1,1)="AA"
a(1,2)="AB"
a(1,2,1)="ABA"
a(1,3,1)="ACA"
a(2,1)="BA"
a(3)="C"
a(3,1)="CA"
I suggest to generate an JSON in the form: 

{"1":["A",{"1":["AA"],"2":["AB",{"1":["ABA"]}],"3":[{"1":["ACA"]}]}],"2":[{"1":["BA"]}],"3":["C",{"1":["CA"]}]}

This may not be the most convenient for the receiving end to read, but it can hold the full information from the array. This can easily be created using a recursive procedure:

 /// Converts an arbitrary array into an JSON-Structure returned
/// as %DynamicObject. Subnodes are read recursively, so there 
/// might be a limit tothe number of levels that can be read.
///
/// Usage example:
/// >set a(1)="A"
/// >set a(1,1)="AA"
/// >set a(1,2)="AB"
/// >set a(1,2,1)="ABA"
/// >set a(1,3,1)="ACA"
/// >set a(2,1)="BA"
/// >set a(3)="C"
/// >set a(3,1)="CA"
///
/// >write $$^Array2JSON(.a).%ToJSON()
/// {"1":["A",{"1":["AA"],"2":["AB",{"1":["ABA"]}],#
/// "3":[{"1":["ACA"]}]}],"2":[{"1":["BA"]}],"3":["C",{"1":["CA"]}]}
///
/// I: &array: reference to the array
///
/// O: JSON: %DynamicObject holding the indices as keys and node
///  values and 
/// subnodes in %DynamicArrays
Array2JSON(&array) Public
{
set JSON = ##class(%DynamicObject).%New()
set key = $order(array(""))
while ( key'="" )
{
// create a new entry
set subJSON = ##class(%DynamicArray).%New()
if ( $get(array(key))'="" )
{
do subJSON.%Push(array(key))
}
if ( $order(array(key,""))'="" )
{
kill subarray
merge subarray = array(key)
set subarrayJSON = $$Array2JSON(.subarray)
do subJSON.%Push(subarrayJSON)
}
do JSON.%Set(key,subJSON)
set key = $order(array(key))
}
return JSON
}