What happened to the original themes?, such as firebird, buckyball, jill, and native.

I tried using them in R2_2.0.2 version, but all the top links disappear.

Maybe that happens because of that change of some time ago, where the top menu is not hardcoded into the templates anymore. You can now choose to assign it like a normal module in Admin > Themes > Layout, to the top, left, right, or bottom.

Are there or will there be any themes like the older versions? I particularly liked the firebird and jill themes.

We've not had time to maintain those themes. They could be updated to work with changes in R2. If you would like to help we'd gladly welcome your contribution. Join us on IRC Freenode channel #bitweaver if you would like to get involved.