Beta means there are new features that haven't been fully tested. Old features are generally unaffected unless otherwise stated. Many apps on the net are in a permanent "beta" phase as features outstrip testing. We try to avoid that when we can, but there's not many working on this (often just me). If you are concerned, just put 2.2 on the menu flash and run new versions from the SD card. If the new version doesn't work out, just remove it and you're back on 2.2.
As to the emulator, I haven't run into anything that doesn't work, but that doesn't mean EVERYTHING works. If you read the neon64 readme, it talks about which mappers are supported, and lists a few games that don't work due to bugs. If you visit the neon64 web page, you'll notice the author quit working on it in 2004. The source is published in case someone else wants to work on it.
