There is a program called TextWiz which is designed to replace multiple rows in text files. You can tell it to replace the same rows (the names) in every file you've selected. I'm not sure if it works with ODFs but if it doesn't you still can save them in text files and then rename the extension to ODF again.
You'd still have to repeat after each update to keep any changes, and Romulan shipnames take about 20-30 rows.
Not long after posting, I remembered the 'include = X' code works in the mod manager. I used that to change the Romulan shipnames. Took a little time, but any future patches will have the name prefix by default.