A lot depends on where the other database is located. If it is on the same server, it is not a big deal.
Actually, it is recommended that for a multi-user database, that you actually "split" the data into two databases; a back-end that that contains all the data tables, and a front-end which contains all queries, forms, reports, and VBA. So in that split environment, ALL the table references in the front-end are linked tables.
So using linked tables should not be a problem, especially in they are on the same network.
I am not quite clear what you mean here. Is your data in SQL, or are you just referring to the SQL View in the query.but when I instead refer to the table with using SQL Query I don't
I am not quite clear what you mean here. Is your data in SQL, or are you just referring to the SQL View in the query.
Regardless, when you link tables, they maintain all the same properties as they do in their native tables (you won't lose primary keys, indexes, or anything like that).
It should be. All the graphical interface does is build the SQL behind the scenes. You can actually create queries by using the graphical interface or by writing the SQL code directly. It shouldn't destroy any of the properties inherent to the tables you are referencing in them.