According to AqBanking's Homepage, since 2013-12-29, the EBICS module is included. This is true for the .tar.gz installer from that website, but not by portage installation: Portage does install aqbanking-cli, aqbanking-config, and aqhbci-tool4 in /usr/bin, but it should install aqebics-tool as well (either by default, or by a new USE flag "ebics").
I added a new use flag in 5.5.1. I have no ebics account to test it though.
Tested - works like a charm ;) Thanks!