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I just wrote a quick script to find unused domain objects. For now, it only tells you they are unused so you can delete them yourself, but it would be simple to make it delete them. The only thing you should need to do is set the value of cmaAddress on the first line if you are using an MDS. It should be the address of a CMA as shown in the output of 'mdsstat'.

cmaAddress=""

portNumber=$(api status | grep "APACHE Gaia Port" | awk '{print $NF}')

showAll() {
IFS=$(printf "\377")
sharedArguments=( --port "${portNumber}" -f json ${cmaAddress:+-d "${cmaAddress}"} -r true show "${1}" details-level full limit 500 )
if ! firstResult=$(mgmt_cli "${sharedArguments[@]}");then return 1;fi
toReturn="$(<<<"${firstResult}" jq -c '.objects[]|.')
";objectCount=$(<<<"${firstResult}" jq -c '.total')
if [ "${objectCount}" -lt 501 ];then echo -n "${toReturn}";return 0;fi
for offsetVal in $(seq 500 500 "${objectCount}" 2>/dev/null | tr "\n" "${IFS}");do
toReturn+="$(mgmt_cli "${sharedArguments[@]}" offset "${offsetVal}" \
| jq -c '.objects[]|.')
";done;echo -n "${toReturn}";}

allDomains="$(showAll dns-domains \
| jq -c '{uuid:.uid,name:.name}')"

echo "" && echo "Working in ${cmaAddress:+CMA }${cmaAddress:-SmartCenter}" && \
echo "${allDomains[@]}" | while read dnsDomain;do
printf "Domain: %s" "$(<<<"${dnsDomain}" jq '.name')"
if [ "0" == "$(mgmt_cli --port "${portNumber}" -f json ${cmaAddress:+-d "${cmaAddress}"} -r true \
where-used uid "$(<<<"${dnsDomain}" jq '.uuid')" \
| jq '."used-directly".total')" ];then
echo " is unused"
else
printf "\33[2K\r"
fi
done

It works by dumping a list of all of the domain objects in the management, then running 'where-used' for each of them. It shows the domain it's currently checking. If the domain is unused, it tells you. If it's used by something, it wipes the line and moves on to the next domain. Here's how the output looks on my lab SmartCenter:

[Expert@DallasSC]# echo "${allDomains[@]}"
{"uuid":"f7bb7e18-4bad-4330-8f2e-4236e6b47382","name":".github.com"}
{"uuid":"df0e50bc-9055-42fd-9d70-216dd7eb73b8","name":".test.com"}
{"uuid":"7eb334af-4088-4665-b26e-b4039f4b862e","name":".time.apple.com"}
{"uuid":"c5ee68ba-c77f-44ce-9907-8001689cbea9","name":".time.windows.com"}
{"uuid":"3ca51f4e-edec-4de3-ae4a-c83c84d0d928","name":".updates.windows.com"}
{"uuid":"c439cf97-4762-4ae7-a759-07c1651d4f2a","name":".www.github.com"}

[Expert@DallasSC]# echo "" && echo "Working in ${cmaAddress:+CMA $cmaAddress}${cmaAddress:-SmartCenter}" && \
> echo "${allDomains[@]}" | while read dnsDomain;do
> printf "Domain: %s" "$(<<<"${dnsDomain}" jq '.name')"
> if [ "0" == "$(mgmt_cli --port "${portNumber}" -f json ${cmaAddress:+-d "${cmaAddress}"} -r true \
> where-used uid "$(<<<"${dnsDomain}" jq '.uuid')" \
> | jq '."used-directly".total')" ];then
> echo " is unused"
> else
> printf "\33[2K\r"
> fi
> done

Working in SmartCenter
Domain: ".test.com" is unused