Based on https://discourse.nixos.org/t/collection-of-nixos-repositories/20941?u=number5 but changed git submodules to git clone.
Example updating script (zsh)
# Nix collections
for d (/nix-collections/*/.git(/)) {
echo "Updating ${d:h:t}..."
command git -C "${d:h}" pull --ff --recurse-submodules --depth 1 --rebase --autostash
}