Good question. data.table can’t delete rows by reference yet.
data.table can add and delete columns by reference since it over-allocates the vector of column pointers, as you know. The plan is to do something similar for rows and allow fast insert and delete. A row delete would use memmove in C to budge up the items (in each and every column) after the deleted rows. Deleting a row in the middle of the table would still be quite inefficient compared to a row store database such as SQL, which is more suited for fast insert and delete of rows wherever those rows are in the table. But still, it would be a lot faster than copying a new large object without the deleted rows.
On the other hand, since column vectors would be over-allocated, rows could be inserted (and deleted) at the end, instantly; e.g., a growing time series.
It’s filed as an issue: Delete rows by reference.