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A lot of software exposes the general "config" or "environment" object too. Thanks to that I haven't encountered many things I couldn't go in my Nix config for already packaged services.
And you can always fall back to Docker in Nix, which has the benefit of all the flexibility and will still declaratively declare your deployments.
So in practice this works out very well in my case, I haven't had to fight Nix (apart from the initial learning curve).