Hi Suri,
Even though, your t-sql contains objects which are not replicated, the records will be deleted from the subscriber.
For example, if your t-sql command is:
delete a
from dbo.tbArticle a
inner join dbo.tbTable t
on a.col = t.col
Under the hood, on the subscriber individual rows would be deleted using primary key as follows:
delete from dbo.tbArticle where pk_col = @id
Regards,
Suresh