kgaurav,
This is the hard way, only possible by editing the code. The file Shortcodes.php which resides in the Functions folder must be edited – open it in Notepad++ and move to line 1369. Remove the (” . $ProdCats[$Category->Category_ID] . “) in the line and the category count will be removed. This applies to version 3.7.0 and most likely will void any warranty the Author offers.