I've heard that apps are left in tact when updating to 2.1, so you should be fine.
But in case you did lose them,
As far as I'm aware, Astro doesn't backup the app data, only the app file it's self. So every app will be a fresh install. I'm also not sure if it will restore the market links for each app.
The only apps that backup data + market links are Titanium Backup (requires root access) and MyBackup Pro (a paid app, but does have a 30 day free trial).
If I were you I'd wait until you hear about the 3 2.1 firmware being released, install MyBackup Pro and then update. That way your 30 day trial will cover the whole process.