Everything in my garden seems to have these holes this year. I think its a beetle making them but I could be wrong. Someone on here will know the answer to your questions though. Welcome to GOY

it is insect /caterpillar daage but dont know which blighter it is, i found small ones having a nibble.
Are you taking cuttings or just keeping them frost free and on the dry side? Dont cut them down as such as they will better protect the lower 'buds' better.

Have a careful look on the underside of the leaves and on the stems for caterpillars. They're often really well camoflaged.

You can leave them out for quite a while longer. I only fleeced up my perlargoniums in December 09 in response to a forecast of prolonged hard frost. Yours are really too small to take any leaves off them yet Peter. Huddle them in a fleece cocoon when the time arrives. Don't let them dry out completely. Give them an airing on sunny mild days. Look at my huge potted plants in my pictures. They overwinter wrapped in fleece. They will bloom all through the winter under the fleece. They are in full bud and bloom at the moment.