Searching the svn-buildpackage manpage for the 3.0 (quilt) format I thought that it wasn't able to apply the patches in debian/patches during build time. Instead I was doing a horrible dance which looked something like svn-buildpackage --svn-export; cd ../build-area/...; debuild. Turns out I was completely wrong.

svn-buildpackage doesn't need to know about the source format. Instead it simply invokes dpkg-buildpackage which will automatically notice that the patches are not applied and apply them before building. That simple!

Thanks to Niels Thykier to point this out to me on IRC.