Using C#
QB Enterprise Contractor Version 6
On a firebreathing PC with everything local (no network access)
The connection was opened in multiuser mode

I tried executing the following SQL

SELECT DISTINCT TemplateRefFullName FROM Invoice

It took over 20 minutes to come back with 4 records, am I doing something wrong?

The query:

SELECT DISTINCT TemplateRefFullName FROM Invoice

will do a full scan of every invoice in your QuickBooks company file back to 1960 if it's there! So the more invoices you have, the longer it will take. This might be a little more practical:

SELECT DISTINCT TemplateRefFullName FROM Invoice where TxnDate>{d'2005-01-01'}

and took less than 4 seconds on my computer. But if you are just looking for Invoice Templates do:

SELECT ListID, Name, IsActive FROM Template where TemplateType = 'Invoice'