ebtables uses RUNPATH to move all of its libraries under $libdir/ebtables/ but portage does not consider that directory when computing REQUIRES and PROVIDES. Simply adding the following to the ebuild cleans things up:
As a side note, there is currently a stable 188.8.131.52 and unstable 184.108.40.206-r1, but both ebuilds are identical. Looks like ebtables.initd-r1 was mistakenly edited in place instead of creating ebtables.initd-r2. Happened ages ago so the extra ebuild probably should just be deleted while updating.
Correction: it isn't that portage doesn't look in the ebtables directory, it is that many of the libraries are missing SONAME. So fixing the build is also an option.