First of all, thank you for the mod!

I've tried to copy non-empty factories and it crashes the game (I mean it just exits without any messages). I don't know whether it should be possible at all, but it certainly should not crash.

Hmm, that's a crash I hoped I wouldn't see again, I suspect it has to do with creating new surfaces during an on_robot_placed event. I'll see to doing something about this, but in the meantime you should not place any factory buildings using robots, neither empty nor full ones. You should remove the buildings from your blueprints.

Just as a note, even if this crash weren't there, if you place down a blueprint of an active factory building, robots will only fill it with an empty factory building, never a used one. To place down a specific factory building using robots, you'll need to shift+click with that building in hand.

So is there any way to copy factory buildings (i.e. reuse them)? For me it's very good abstraction to build upon

Even shift-right click, shift-left click copy will be good (even if it creates ghosts inside)

You can always use blueprints to copy the entire interior of a factory building. The copy-pasting mechanism is only going to be used to copy-paste connection settings, once I get around to implementing that.

Yes, but it won't help with nested factories. I think of factories as useful abstractions, hiding their implementation within as a black box, not just space saving technique.