This Python 3.0 script (courtesy of Dunto) finds any Starbound mods installed from the Steam workshop and adds them to the search path in sbinit.config.

Starbound Workshop Mod Loader

#!/usr/bin/python

# From: http://community.playstarbound.com/threads/steam-workshop-mod-loader.119587/
# And: https://gist.github.com/Dunto/4f1396a784802bfbda12a029796c0f4b

# That was before Dunto sent this own valuable content into the memory hole.
# So here it is, back from the grave, because as I'm sure you know, the
# Internet interprets censorship as damage and routes around it.

# I have edited it to exclude workshop mod directories that are empty.

# ~~~

# This script will allow Starbound to load Steam workshop mods without moving
# files around.  It works by updating the sbinit.config file to include the
# Steam workshop mod folders.  Since Starbound will not look deeper than one
# folder level for for mods, each mod's workshop folder must be specified.
# Running this script synchronizes the sbinit.config mod search paths with 
# the folders in the Steam workshop downloads folder for Starbound.
# This script only needs to be run if you add or remove workshop mods,
# it does not need to be run if your current mods simply update.

# Copyright 2016 Dunto, see below for license information.
# This script was written as a quick solution to a personal requirement,
# it may or may not be improved on as time passes.  I make no promises
# as to whether it will work properly for you or not.

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>

import os
import json

def getSbInstallPath():
    if os.name == 'posix':
        return os.path.expanduser("~/.steam/steam/steamapps/common/Starbound/")
    elif os.name == 'nt':
        return os.path.expandvars("%ProgramFiles(x86)%\\Steam\\steamapps\\common\\Starbound\\")
    else:
        raise Exception("Error: Unable to determine operating system!")

def getOsDirs():
    if os.name == 'posix':
        return ["linux", "osx"]
    elif os.name == 'nt':
        return ["win32", "win64"]
    else:
        raise Exception("Error: Unable to determine operating system!")

def loadInitConfig(init_path):
    INIT_FP = open(os.path.join(init_path, "sbinit.config"), 'r')
    init_data = json.load(INIT_FP)
    INIT_FP.close()
    return init_data

def storeInitConfig(init_data, init_path):
    INIT_FP = open(os.path.join(init_path, "sbinit.config"), 'w')
    json.dump(init_data, INIT_FP, indent=2)
    INIT_FP.close()
    

# begin main
STARBOUND_INSTALL_PATH = getSbInstallPath()
STEAM_STARBOUND_WORKSHOP_PATH = os.path.normpath(os.path.join(STARBOUND_INSTALL_PATH,"..","..","workshop","content","211820"))
STEAM_STARBOUND_WORKSHOP_RELPATH = os.path.join("..","..","..","workshop","content","211820")
STARBOUND_BASE_ASSET_DIRS = ["../assets", "../mods"]

# If you have a custom Steam library location, you'll need to manually set 
# these variables to the correct folder paths and uncomment them.
#STARBOUND_INSTALL_PATH="/path/to/starbound/folder"
#STEAM_STARBOUND_WORKSHOP_PATH="/path/to/steam/workshop/content/211820/folder"

#for os_dir in getOsDirs():
for os_dir in ["linux", "osx", "win32", "win64"]:
    # Load sbinit.config
    init_data = loadInitConfig(os.path.join(STARBOUND_INSTALL_PATH, os_dir))
    # Remove all mod folder entries and re-add base entries
    init_data["assetDirectories"] = []
    for base_dir in STARBOUND_BASE_ASSET_DIRS:
        init_data["assetDirectories"].append(os.path.normpath(base_dir))
    # Add workshop mod entries
    if os.path.isdir(STEAM_STARBOUND_WORKSHOP_PATH):
        for entry in os.listdir(STEAM_STARBOUND_WORKSHOP_PATH):
            if os.path.isdir(os.path.join(STEAM_STARBOUND_WORKSHOP_PATH, entry)):
                if os.listdir(os.path.join(STEAM_STARBOUND_WORKSHOP_PATH, entry)):
                    init_data["assetDirectories"].append(os.path.join(STEAM_STARBOUND_WORKSHOP_RELPATH, entry))
    # Store updated sbinit.config
    storeInitConfig(init_data, os.path.join(STARBOUND_INSTALL_PATH, os_dir))

print("\nUpdated Starbound with Steam workshop mods!\n")
os.system("pause")
# end main