Summary:
Microsoft SQL Server 2005 introduces the concept of a synonym. A synonym is an alternative name for a schema-scoped object. Client applications can use a single-part name to reference a base object by using a synonym instead of using a two-part, three-part, or four-part name to reference the base object.
Strategy Architect can access synonyms just like tables from database. In order for this access to be available some changes have to be made in the construction of SQL used by warehouse catalog.
1) In Strategy Desktop 9.3.x /Developer 9.4.x go to "Schema" menu and click "Warehouse Catalog..."

2) On Warehouse Catalog, access the read settings by going to Options > Catalog Read Settings > Settings:

3) Change SQL for tables and then for columns inserting the following SQL statements:
TABLES:
SELECT DISTINCT S.name NAME_SPACE, T.name TAB_NAME
FROM sys.all_objects T JOIN sys.schemas S on T.schema_id = S.schema_id
WHERE T.type IN ('U', 'V', 'SN') AND S.name IN ('dbo', N'#Login_Name#')
SELECT S.name NAME_SPACE, T.name TAB_NAME, C.name COL_NAME, C.user_type_id DATA_TYPE, C.max_length DATA_LEN, C.precision DATA_PREC, C.scale DATA_SCALE
FROM sys.all_objects T
JOIN sys.columns C ON T.object_id = C.object_id
JOIN sys.schemas S ON T.schema_id = S.schema_id
WHERE T.name in (#TABLE_LIST#)
UNION
SELECT S.name NAME_SPACE, SY.name TAB_NAME, C.name COL_NAME,
C.user_type_id DATA_TYPE, C.max_length DATA_LEN, C.precision DATA_PREC, C.scale DATA_SCALE
FROM sys.all_objects T
JOIN sys.columns C ON T.object_id = C.object_id
JOIN sys.schemas S ON T.schema_id = S.schema_id
JOIN sys.synonyms SY ON T.name = (SUBSTRING(SUBSTRING(SY.base_object_name,
CHARINDEX('.', SY.base_object_name)+ 2,
len(SY.base_object_name)-CHARINDEX('[', SY.base_object_name)
), CHARINDEX('[',SUBSTRING(SY.base_object_name,
CHARINDEX('.', SY.base_object_name)+ 2,
len(SY.base_object_name)-CHARINDEX('[', SY.base_object_name)
)) + 1, LEN(SUBSTRING(SY.base_object_name,
CHARINDEX('.', SY.base_object_name)+ 2,
len(SY.base_object_name)-CHARINDEX('[', SY.base_object_name)
)) - CHARINDEX('[',SUBSTRING(SY.base_object_name,
CHARINDEX('.', SY.base_object_name)+ 2,
len(SY.base_object_name)-CHARINDEX('[', SY.base_object_name)
)) -1))