Yes I've experienced the same issue with my Pioneer deck, after updating to ios4, bluetooth hands free, and audio streaming hasn't been pairing properly.
After many attempts to repair both hands free and audio, I gave up.
Since ios4 really slowed down my 3G device, I decided to just rollback the device to ios3.1.3 (Which is not officially supported by apple.) You can find articles on how to do this on lifehacker.com But beware, when you do the rollback, all your app settings (login credentials, game records) are all reset. You also must resync with iTunes to get all your apps back, so make sure you have a backup.
After the rollback, everything seems to working fine. Bluetooth now pairs with handsfree and audio automatically consistently, the UI on the device is more responsive. So if you like your iphone 3g, be kind to it and keep it at ios3.1.3 🙂