By default, Gentoo only compiles the GnuTLS libs without tools:
In order to compile these, the local USE=tools flag must be set. But only then, net-libs/gnutls[tools] has a BDEPEND on sys-devel/autogen, which in turn has a depend on GUILE.
When compiling the default (libs-only), there is no such dependency in the Gentoo emake.
Since the default source of GnuTLS (>=3.6.7) does not rely on GUILE/autogen, and its tools can be compiled without GUILE (even setting USE=tools and emerge --nodeps works), this seems to be a bogus dependency and thus be removed.