You can use a PHP ternary operator written in the Magmi value replacer advanced syntax to append the value if the store2 column value exists.
[{item.store1}]/{item.subcat}{{(!empty({item.store2}) ? ';;['.{item.store2}.']/'.{item.subcat} : '')}}
This basically says if item.store2
is not empty, then return ;;[{item.store2}]/{item.subcat}
In actual PHP, this would look more like
(!empty($item['store2']) ? ';;['.$item['store2'].']/'.$item['subcat'] : '');