Do I need to use a wood hardener when using Bondo to fix window rot?

Yes, I would recommend a wood hardener. It makes the mushy part solid again. Of course you could just dig out all the mushy wood and then bondo. I don't believe the hardener does anything to prevent further rot except seal it in. By the way Bondo is not an epoxy filler, but a polyester resin. It will work fine to fill but you should definitely paint it thoroughly because it will absorb moisture.