I forgot to respond to your second question there. The short answer is it shouldn't ever be a limitation. They're saying there's not a place to plug in a flash sync cord except the bottom. This really isn't an issue because you can put your D90 in commander mode and control the SB-600 wirelessly and it meters through the lens to set flash output (Nikon's wireless flash control is really amazing to me). If you ever absolutely need to have wired flash triggering off-camera, you can buy a cable like the SC-29 and you keep through-the-lens flash metering, as well. Personally, I think it's just too much hassle when you can do it without a cable. I own a flash sync cord and it's mostly become a toy for my kids. Sometimes I'll use it to set up my flash to trigger studio lights so I don't have to deal with the preflash.
Do you mean that you can control Sb-600 through a wireless controller like Nikon ML-L3 Wireless Remote Control or did you mean that the SB-600 would be controlled by D-90 and D-90 would be trigreed by ML-L3?