Welcome to the forum. Judging by your many comments on the HPV community forum, many of which are reassuring to other users with their own questions, you have done a lot of research on these issues and are quite knowledgeable. For some of your questions, you may know as much as I do. Because genital warts are generally considered a minor health problem (regardless of the emotional distress they can cause), there has not been much research. Most of what we know is based on clinical observation and common sense, not on firm data. That said, I'll do my best.
1) Almost all warts, whether genital or the hand or foot warts common in childhood, clear up eventually on their own, even if never treated. When untreated, they appear to "melt away" -- i.e. people just notice one day that they are gone. But I suppose sometimes they may dry up and flake off. If and when new warts appear, it probably usually just means the virus has persisted in tissues and for some reason the immune system has failed to keep them in check as well as it once did.
2) STD experts generally assume infectiousness for partners depends in part on viral load, i.e. the amount of active, transmissible virus in infected tissues; and that viral load likely is higher in overt warts than in asymptomatic infection. We hope, therefore, that treating overt warts reduces the potential for transmission to partners. However, I stress there are absolutely no data on this. It's not much more than educated (and hopeful) guesswork.
3) Anti-HPV treatment has no effect on existing scars. Over time, scars in general tend to soften and become less prominent. In severe cases, special treatments might improve them. This is an issue for a dermatologist; I have no experience with this.
4) The best estimate is that 60-70% of people who acquire HPV 6 or 11 develop visible warts. That leaves a large minority (30-40%) who have only asymptomatic infections. Typically it takes 6-12 months before visible warts appear, and they rarely show up before 3 months. Therefore, some apparently asymptomatic infections may simply appear late -- sometimes long after the exposure.
5) Neither of the HPV vaccines (Gardasil or Cervarix) has any effect whatsoever on existing warts or HPV infection.
I hope this helps. Best wishes-- HHH, MD
PS: sorry about the mistype for the fifth question...now I'm expecting your answer for all of my questions! Thanks! ^^