Ship templates was a new feature when DA was release, so ship templates only work with DA and TA. With DL, it was common practice to make a blank ship with the desired jewelery, and then upgrade the design whenever you wanted a new ship of the given model. By making the ship empty, you could always have access to a design regardless of your miniturization level.
As for DA and TA, duplicate designs seem to be a common event. You can't make a ship template of a design without actually designing the said ship as an actual ship. Atleast, I haven't been able to do so. Make a point of only deleting the buildable ship, and not the template and you should be fine (though it does take extra clicking than you probally want).
Let me know if this answers your questions.
