I'm hoping the vet, Dr. Lee, will be around to answer your question because there are other possibilities. But if herpes is suspected, it never goes away, like many other viruses, and when it flares up (stress is a big factor), secondary infection is almost a certainty and yes, these must be treated with antibiotics, to withold them would be to prolong her suffering and invite other, more serious infections. So please treat her, whenever the vet says it is necessary.
Herpes is contagious, as are many of the other viruses, although not as contageous as a cold. But the brother, I'm afraid, may also have it, since it is common among kittens from the same litter. Perhaps he is physically a little stronger so doesn't get sick as often.
I have a cat with herpes and he leads a very normal, happy life, although he is miserable during flare-ups, for which he always gets antibiotics.
Stress is a huge factor. Are they in a comfortable, non-threatening situation, no problems with dogs, other cats, small children (sorry). Does she stay inside (highly recommended)? You don't have to treat them like invalids, but safety is a big issue for cats, their number one stressor after not getting enough food.
Make sure they eat the best food you can afford, good nutrition is important.
I would put them both on lysine for a good long time, maybe a couple of months, even when they are not sick. It boosts their immune system. Try the capsules meant for humans, they are not expensive (the kind the vet sells definitely is). Make sure it is pure lysine, no additives. The kind I buy at the health food store is in 250 mg capsules that you empty into their food, twice a day.
Don't despair, kitties with viruses are not necessarily doomed, they just need a little extra care.