Thank you John, that explains quite a bit, couldn't properly work that way. Reverting to the "simple" bootloader now resulted even in a usual, slow blinking LED. I also fiddled with the fuses, setting hfuse to 0xDE instead 0xDA; writing the lockbits 0x0F to make sure they're correct.
It's really weird: Giving the Nano a kickstart via AVRdude makes the sketch work one time. Using USB to connect the Nano standalone again makes it play dead. I think I have electrically broken something. I do have some equipment, but that is not good enough for debugging the µC itself (DSO Nano, VC97 - can show a lot for own PCBs/designs at lower frequencies). I'm waiting for a EZ-USB based logic analyzer now but there I wouldn't even know which protocol to dissect 
I guess I could at least see up to 24MHz the toggling of the lines.
It's no drama, only a bit sad - that was my first Arduino PCB, a very solid made one, nice LEDs, proper soldering, not like some of those cheap clones.