Hello there!

I'm little bit confused, 'cause in EnderIO 2.2 we can use Farming Station to farm oreberry bushes. But now, there is no way how to user farming station this way. Is it bug in your code, or between my chair and keyboard?

It still should work. Can you describe and/or screenshot what you are doing?

It says no seed but where I have to put seeds, when oreberry has no seeds...? And second thing - i used hoe, hoe was destroying but nothing happend.

The machine has no need for seeds to start working. Once it is in range of a oreberry bush it will start collecting it even without seeds, it will, however, still accuse there are no seeds. This will work with flowers from vanilla as well in case you have a farm of those.
I've tested the machine with version 2.3.0.421 with several mods.

And what kind of tool you have to use? :-)

You can use any kind of hoe (as far as I've seen, it registers pretty much any hoe that has durability).
Edit: For a list of the supported hoes, you can find it in the EnderIO.cfg starting from line 364 (or around that number). You can also add your own hoes there if you'd like...