The reason is that LDFLAGS should _not_ be used for libraries, as it has to be positioned before the list of objects to link together, while libraries should go after. This mistake in commandline is what causes as-needed to either fail or not apply at all (if LDFLAGS are put at the end). Please fix your package not to pass libraries through LDFLAGS.
Hi, numpy build system is very unstable and does not respect many flags, not only LDFLAGS. Upstream is working slowly in using scons, meanwhile the append-ldflags in the ebuild is necessary as a hack. See http://projects.scipy.org/numpy/ticket/573 and others. Please re-open with a build log if you see your LDFLAGS flags don't get passed. Thanks.
Problem is that they get passed with e.g. -Wl,--as-needed which passing libraries with append-ldflags breaks.
Nevermind, should have checked the upstream bug before reopening.