This does appear to be a limitation, though I can't find this documented anywhere...

But this relates the to number of nodes you list in the modify expression. Not the nodes in the document!

So I have to ask:

Why are you explicitly listing out all the nodes in your XQuery expression? You can use wildcards to match nodes. So in your example you can replace the whole looping nonsense building v_clob_upd_sql with:

declare default element namespace "http://www.mywrb.com/test/mys";  (: :)  
  copy $tmp := $inxml modify (
    (for $i in $tmp/datapacket/data/sec/row/* return replace value of node $i with xs:integer($i + 1))
  ) 
  return $tmp

This enables you to update documents with far more than 2426 nodes:

DECLARE 
  v_data_xml CLOB; 
  v_clob_upd_sql VARCHAR2(1000); 
  v_bool BOOLEAN := false; 
  LV_OUT_XML XMLTYPE; 
  lv_number_of_nodes number := 10000; 
BEGIN 
 
 -- Variable holding the data XML  
  v_data_xml := q'[<?xml version="1.0" encoding="UTF-8"?>    
                  <mys:datapacket                    
                  xmlns:html="http://www.w3.org/1999/xhtml"                    
                  xmlns:mys="http://www.mywrb.com/test/mys">      
                  <mys:data>     
                  <mys:sec>     
                  ]'; 
  FOR I IN 1..lv_number_of_nodes 
  LOOP 
    dbms_lob.append(v_data_xml,'<mys:row><mys:pk'||i||'>'||i||'</mys:pk'||i||'></mys:row>'); 
  END LOOP; 
  DBMS_LOb.APPEND(v_data_xml,'</mys:sec></mys:data></mys:datapacket>'); 
   
  -- XMLQUERY to update all the nodes in the data XML  
  v_clob_upd_sql := 'declare default element namespace "http://www.mywrb.com/test/mys";  (: :)  
  copy $tmp := $inxml modify (
    (for $i in $tmp/datapacket/data/sec/row/* return replace value of node $i with xs:integer($i + 1))
  ) 
  return $tmp';
   
  SELECT 
    xmlquery( v_clob_upd_sql passing xmltype(v_data_xml) AS "inxml" returning content) 
  INTO lv_out_xml 
  FROM dual; 
  dbms_output.put_line(substr(lv_out_xml.getClobVal(), 1, 400));
END;
/

<?xml version="1.0" encoding="UTF-8"?>
<mys:datapacket xmlns:mys="http://www.mywrb.com/test/mys" xmlns:html="http://www.w3.org/1999/xhtml">
  <mys:data>
    <mys:sec>
      <mys:row>
        <mys:pk1>2</mys:pk1>
      </mys:row>
      <mys:row>
        <mys:pk2>3</mys:pk2>
      </mys:row>
      <mys:row>
        <mys:pk3>4</mys:pk3>
      </mys:row>
      <mys:row>
        <mys:pk4>5</mys:pk4>
      </mys:row>
      <mys:row>
        <mys:pk5>6</mys:pk5>
      </mys:row>
      <mys:row>
        <mys:pk6>7</mys:pk6>
      </mys:row>
      <mys:ro