bash shell script two variables in for loop

I am not certain I understand your need for a single loop. You could get the same output using two consecutive loops like this

for MASTER_CLUSTER in $MASTER_CLUSTERS

    do
          echo "Master cluster boxes are ${!MASTER_CLUSTER}"
    done

for SLAVE_CLUSTER in $SLAVE_CLUSTERS
    do
          echo "Slave cluster boxes are ${!SLAVE_CLUSTER}"
    done

or if the values must be alternated then

for MASTER_CLUSTER in $MASTER_CLUSTERS
    do 
    echo "Master cluster boxes are ${!MASTER_CLUSTER}"
    for SLAVE_CLUSTER in $SLAVE_CLUSTERS
       do
          echo "Slave cluster boxes are ${!SLAVE_CLUSTER}"
       done
    done

Extending my answer based on the OP's clarification. Again, you can use an array:

$ cat /tmp/foo.sh
#/bin/bash

# Sample values from OP
export MASTER_CLUSTER_1="MASTER1 MASTER2"
export MASTER_CLUSTER_2="MASTER3 MASTER4" # (edited to be unique)
export SLAVE_CLUSTER_1="SLAVE1 SLAVE2 SLAVE3 SLAVE4"
export SLAVE_CLUSTER_2="SLAVE5 SLAVE6 SLAVE7 SLAVE8" # (edited to be unique)

# Create two arrays, one for masters and one for slaves.  Each array has
# two elements -- strings containing space delimited hosts
declare -a master_array=( "${MASTER_CLUSTER_1}" "${MASTER_CLUSTER_2}" )
declare -a slave_array=( "${SLAVE_CLUSTER_1}" "${SLAVE_CLUSTER_2}" )

# For this to work, both arrays need to have the same number of elements
if [[ "${#master_array[@]}" == ${#slave_array[@]} ]]; then
    for ((i = 0; i < ${#master_array[@]}; ++i)); do
        echo "master: ${master_array[$i]}, slave: ${slave_array[$i]}"
    done
fi

Sample output:

$ bash /tmp/foo.sh
master: MASTER1 MASTER2, slave: SLAVE1 SLAVE2 SLAVE3 SLAVE4
master: MASTER3 MASTER4, slave: SLAVE5 SLAVE6 SLAVE7 SLAVE8