Generating two .csv files from named parameters
Everything looked pretty good in general, until I got to the (let [output_directory ... part, then your indentation got all wonky! Part of the problem is that there are a couple of really long lines, and it's difficult to keep them short when you're nested so many layers deep into an S-expression. Shortening your lines and making sure that everything lines up from line-to-line in an intuitive way will solve this.

First of all, I believe it is idiomatic to include all your use/require/import statements within the namespace definition, like so:

(ns my_cli_clojure.core
  (:require [clojure.data.csv :as csv]
            [clojure.java.io :as io]
            [me.raynes.fs :as fs]
            [clojure.tools.cli :refer [cli] :as c]
            [clojure.string :as s])
  (:gen-class :main true))


Notice that I added [clojure.string :as s] -- this abbrevation will come in handy in shortening some of the later lines, in which you have a lot of fully-qualified references to clojure.string methods.

Next, just an aesthetic spacing tweak here:

(defn write-csv-data [&amp; {:keys [data outfile] :or {data "", outfile ""}}]
  (csv/write-csv outfile data))


Your code was fine, I just find my version easier to read at a glance. I generally try to avoid using line-breaks whenever the code I'm writing looks sufficiently compact on less lines. When the lines start getting long, I will think more about where it would make the most sense to break them up. (I also renamed write_csv_data to write-csv-data; it's idiomatic in Clojure to name symbols using hyphens instead of underscores)

More spacing adjustments here:

(defn -main [&amp; args]
  (let [[options args banner]
        (c/cli args
               ["-d" "-dome" "Dome Identifier" :default "dome1"]
               ["-p" "-principal" "Principal code" :default "kraft"]
               ["-o" "-output-directory" "Output file" :default "."]
               ["-h" "-help" "Show Help" :flag true :default false])]


Here is how I would tackle the part at the end:

(let [out-dir (:output-directory options)]
  (if-not (fs/exists? out-dir)
    (fs/mkdirs out-dir))
  (doseq [n (s/split (:dome options) #",")]
    (let [dome-id (first (s/split n #"-"))]
      (with-open [out-file (io/writer (str out-dir "/" dome-id ".csv"))]
        (write-csv-data :data [["dome_identifier" "name"]
                               [dome-id (last (s/split n #"-"))]] 
                        :outfile out-file))
      (with-open [dome-principal-file 
                  (io/writer (str out-dir "/dome_principal." dome-id ".csv"))]
        (write-csv-data :data [["dome_identifier" "principal_code" 
                                "currency_code" "active" "latitude" "longitude"]
                               [dome-id (:principal options) "" "t" "" ""]] 
                        :outfile dome-principal-file)))))))


Changes:


I shortened a few symbol names, like output_directory => out-dir and dome_identifier => dome-id. 
I changed the two parts with the pattern like (s/join "/" [out-dir (s/join "." [dome-id "csv"])]) to (str out-dir "/" dome-id ".csv"), which is more concise and easier to read. Keep it simple!
I simplified (first (reverse (s/split n #"-"))) to (last (s/split n #"-")).
There's a part of your code where you created a list of strings by doing something like this: (s/split "first-string second-string third-string fourth-string" #"\s+"). That's clever, but the downside is that it leaves you with a long string that you can't break in order to shorten your lines. In this case, I think it makes more sense just to type e.g. ["first-string" "second-string" "third-string" "fourth-string"].


Hope that helps!