The capacitance on the crystal will 'pull' the clock frequency slightly, if you need a really precise clock you use trimmer caps and adjust them until the crystal outputs the exact frequency you need. I'd use whichever you have available, if in doubt purchase two sets of capacitors, and test them both ways, the exact value you use is actually up to what the crystal maker suggests. It shouldn't be that critical though. The zeners look like a safety measure for both the USB line and the AVR itself, to protect the chip and bus from transients they're not absolutely required, but not a bad idea.
The LV version probably runs on a lower voltage, and may or may not work with normal voltage devices. I've found the voltage an AVR runs on once the oscilator is started is actually far outside it's listed specs. The LV versions are just garunteed to start and operate normally under a lower voltage range. All LV parts should be programmable using a normal voltage programmer in general, but I'm not sure what specific chips you're talking about so that piece of advice should be taken with a grain of salt.