Welcome to the STD forum. I'll try to help. However, these questions have been discussed many times on this forum; for more detailed information, use the search link.
In general, the STDs and the bacteria, viruses, and other organisms that cause them evolved in parallel with human evolution in a way that makes very intimate contact a requirement for transmission. In general, that requires insertive sex -- i.e. a penis inside another person's vagina, rectum, or mouth. Although rare transmissions occur through genital apposition without penetration, it is very uncommon. For practical purposes there is never any risk for any STD from genital contact with hands or other skin, from non-genital body rubbing, or kissing.
1) Yes there is some transmission from genital apposition without penetration, with HPV and herpes being the most likely. Syphilis can be transmitted this way, but since syphilis is rare in most populations, this is rarely any risk.
2) No STDs are acquired through intact latex or polyurethane, and probably only rarely through intact nature membrane condoms. But as you suggest yourself, some STDs are transmitted primarily by skin-to-skin contact, which occurs to a certain extent despite use of the male condom. (The female condom may prevent more skin-skin contact.) However, despite this, during any particular sexual exposure, properly applied condoms that do not break probably is around 90% protective against HSV and HPV -- i.e. very good but not perfect. By contrast, protection is virtually 100% for those STDs transmitted through infected secretions rather than skin -- i.e. gonorrhea, chlamydia, HIV, hepatitis.
3) Small holes and microscopic condom leaks are an urban myth. If they occur at all they are rare, and they probably almost never account for STD transmission despite condom use. As you suggest yourself, condom failure is generall all-or-nothing: an overt rupture that is impossible to miss. And of course improper use is a common reason condoms don't work. Mostly that means partial contact; for example, some users mistakenly believe STDs and pregnancy are acquired only through semen, so they have unprotected sex part of the time and apply the condom only for ejaculation.
I'll be happy to answer a brief follow-up question if necessary. But as implied above, these issue have been discussed a lot, so please search the forum -- most likely anything you don't understand has been covered. Here is one thread on condom use to get you started: http://www.medhelp.org/posts/STDs/How-safe-are-condoms-when-used-correctly/show/665887
Best regards. Stay safe-- HHH, MD