The same way you do it in other db system, you can use the name of the db for identifying double named tables. unique tablenames can used directly.
select * from ttt.table_name;
or if table name in all attached databases is unique
select * from my_unique_table_name;
But I think the of of sqlite-shell is only for manual lookup or manual data manipulation and therefor this way is more inconsequential
normally you would use sqlite-command-line in a script