Hi Sergio,
I am not sure if this works. The database and the file system are sort of synchronized. You would also have to delete the lucene index. I don't recommend to delete anything manually in the database. And, btw, the files in the alf_data won't be removed.
If you delete something via SOAP, the deleted items are placed in the "recycle bin", too. So, there might be a solution to delete the items finally.
I don't know anything about deleting a store, maybe one of the developers could help us here.
Regards
Christian