The flash will go off, but it shouldn't effect the photo in most cases (in some instances it will be however, such as shooting close to reflecting objects). Nikon does make a flash blocker that works well.
But yes, you can control the flash units (SB-600, SB-800, SB-700, SB-900) wirelessly...
That's not the only difference, actually... there's slightly better ISO performance (not much, but a little), a little different button configuration (more notable center 'ok' button for example, 2 card slots (one CF and one SD), and a few other small items.
The biggest difference to me is...
Another vote for the D300(s) or D7000, I own both and they are simply awesome cameras. The D7000 has much better performance in the upper ISO range, which is one reason I bought it.
D300(s) can pop off 7-8 fps, D7000 does 6 - D90 does 4.5 if I remember right.
I've also owned the D90, and...
The D90 can control it remotely without any extra devices, and the SB-700 can also be the wireless commander if you wish.
That said, it would need to be within site/range of course. Some people use Pocket Wizards or eBay knock-offs that work quite well but I believe you lose the iTTL...
You must be a Canon shooter? Don't fret, you bought it for a reason and I'm sure you're enjoying it (I hope). This didn't turn into anything but facts... I found it interesting that the D700 is handling both extremes quite well.
It will work the same way, but the field of view will be different (you won't get as much of the scene in the frame).
I can't recommend the Sigma 18-50 f/2.8 enough for what you're wanting to do, it's an incredible lens and rather versatile as well. Bokeh is great and it can be sharp as a...
Fall Colors by Light Artisan Photography, on Flickr
Canon G12 vs Nikon D300s by Light Artisan Photography, on Flickr
At The Reservoir by Light Artisan Photography, on Flickr
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