Heat Shielding: The space shuttle was made to withstand atmospheric reentry, obviously, but this also allowed it to withstand something the engineers had never thought it would ever have to contend with, Godzilla's Atomic Breath. The space shuttle took several seconds to a minute of the monster king's heat ray before being up to pull out and only took minimal damage. It would later take several seconds of the Fire Dragon's flames, again with minimal damage.
Freezer Missiles: Like the Super-X3 in the Heisei era, the shuttle was able to be armed with freezer missiles, likely to put out fires on moon bases too large to normally be put out. Though not intended as a weapon they were very effective against the Fire Dragon, first putting out the flames, with follow up shots causing it's power source to fail, making it crash and shatter like glass.
Transportation: The shuttle was able to transport Exploration Cars armed with laser defense cannons. Although it is meant for space travel and exploration, the shuttle could be used to transport weapons, troops or bombs should the need ever raise.
In conclusion the Moonlight-SY3 is like a Showa prototype of the Heisei era's Super-X weapons. Like the Super-X 1 and 3, it was not originally meant for combat but proved to well built in not only surviving energy weapons but as an effective means of putting an invasion on ice.