1. I'm positive it's an email address, or that's at least what it's referred to most of the time. You can check out this topic: http://www.detectiveconanworld.com/forum/topic/5521-is-the-bosss-number-a-phone-number-or-an-email-address/
2. The number is #969#6261 (not 0858, Tottori), though it sounds similar to a Kurayoshi area code (Gosho also used this number in particular to prevent prank calls if I'm not mistaken, I think he also chose the number upon calling home) - Gosho said that there is no connection between the two, although we don't really know if he is completely serious or not. There is some more information in the translating interview topic regarding this.
3. The number is mentioned afterwards, but I'm not sure exactly when the last time Conan referenced it was? I think it's brought up again in the Clash of Red and Black series. As mentioned before, there are quite a few people that know the number.