meanwhile I found out that I can access EEPROM, it is just empty and have loaded the cape.eeprom file into it.
After a reboot that works:
root@qbone:~# cat /sys/devices/platform/bone_capemgr/slots
0: P----- -1 UniBone,00B0,Hoppe,UniBone
1: PF---- -1
2: PF---- -1
3: PF---- -1
4: P-O-L- 0 Override Board Name,00B0,Override Manuf,UniBone
But still the issue that the board is not booting with power on connector J8 only. Booting is only possible when applying power to both J8 and the Mini-USB of BBB.