I dunno. I think the standard is Word or some other word processors like open office (I'll have to check); but Word is the standard. Indesign handles importing the Word footnotes pretty well.Let me know if there is something else that might help. I'm sure you're much rather your time be spent doing something more productive than a repetitive formatting or parsing. Do you do all the footnotes in Word and then import a Word document into InDesign?
Word is a good tool for being able to see some things visually but it's hard to automate (maybe David can help with some macros). But if InDesign can import a different format then that might be helpful.