Yesterday I released version 4 of dh-autoreconf, fixing two bugs, and introducing a new feature: Patching ltmain.sh to make -Wl,–as-needed work.
For this new feature, run dh_autoreconf with the –as-needed option. dh_autoreconf will then patch all ltmain.sh equal to the system one (which should be all ltmain.sh files if libtoolize ran before or via dh_autoreconf). On clean, dh_autoreconf_clean reverses the patch again.
So, if your package runs autoreconf, and patches ltmain.sh via a patch you can now do this automatically via dh-autoreconf and be future-proof.
The only problem is that this might break once the patch no longer applies to libtool, at which point I need to update the package to include an updated patch. A solution for this problem would be to include the patch in libtool itself, as I proposed in Bug#347650.
In case this works well, the option could also become the default which would make things even easier.