We are implementing a new Journal Entry Approval Workflow. We have a number of saved csv import templates that don't have the "Run Server SuiteScript and trigger WorkFlows" option checked. Do we have to go in to each one and check it and re-save it?

yep, don't think there is csv import for csv import

That's a shame. I even checked the preference for it in CSV Import Preferences but I guess that isn't retroactive?

I guess that isn't retroactive

Nope. Theoretically you could try to script it (if that record is even scriptable?), but unless you have hundreds, just doing it manually would likely be quicker.