The "bullet holes" I think are just holes for the steps/ladder to go in.
As for the 1 missile dilemma - who knows? they were part of the ongoing operations over libya so it may be possible that they used it - having said that though a couple of FAF Mirage F1s landed about a week before these because the refueling tanker developed issues so they were running out of fuel (actually the damaged one was one of that pair as well - it seems to have an affection for Malta hehe) and they also had one missile missing.
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