The point was to install the deps into my project tree, instead of putting everything into /gnu, but to think of it that's not actually much of a problem, it's just personal preference/bikeshedding.
"Installing" a package with Guix really just means that it is referenced through a link. /gnu is just a cache for "evaluated" package recipes. You could create a profile that contains your symlinks to the items in the store wherever you want, including the currenty directory.
guix package -p $(pwd)/.guix-profile -i what ever you want
Programmes in this profile can then be executed like so:
./.guix-profile/bin/what
But that's not necessary when you could just use `guix environment` and enter a shell where everything is already hooked up.
I'm installing it and see how it goes, thanks.