Yes you should be able to install the new version 2.5 over the one you have installed 2.44.14. In the latest versions of the cart 2.44.16 and 2.5 there is a new categories module and the cart now supports sub categories. In order to support sub categories we had to change the table structure of the category and product table a bit and there is a new table called smith_categoryproduct to support a many to many relationship between categories and products. In the sqlprovider install, I added an insert statement to populate the new categoryproducts table:
insert into dnn_smith_categoryproduct (categoryid, productid)
select categoryid, productid from dnn_smith_products
You should be good to go installing over the old module but remember its always a good idea to backup your dnn install and database before installing new modules