I totally sympathize with you on the 2 times a month thing. When new drivers come out, I grind on my system too until the damn thing works right. But you should be able to whittle that down to once a month or a possible once every two months. At the most, don't expect anything greater than once every 6 months. If you don't have to completely wipe Nes98/NesME every 6 months, you're not using your computer correctly.
The only real problem with drives is where you are doing the majority of your reading and writing. Reformating is just a sweep of writing, so it's just as 'destructive' as if you had wrote a file to the drive. Most likely, when you start getting errors, it'll be at the very start of your drive where the windows system files are always stored. If you're keeping your hard drive cool, it'll last 5 years at least before you start getting errors.